dbSNP rs3748643: CCDC163:c.-422C>A (chr1-45500031-G-T) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001102601.3(CCDC163):c.-422C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 519,220 control chromosomes in the GnomAD database, including 135,946 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.74 ( 41787 hom., cov: 31)

Exomes 𝑓: 0.71 ( 94159 hom. )

Consequence

CCDC163
NM_001102601.3 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.682

Publications

20 publications found

Variant links:

Genes affected

CCDC163 (HGNC:27003): (CCDC163 homolog) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

CCDC163 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BP6

Variant 1-45500031-G-T is Benign according to our data. Variant chr1-45500031-G-T is described in ClinVar as Benign. ClinVar VariationId is 684370.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001102601.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CCDC163	NM_001102601.3	MANE Select	c.-422C>A	5_prime_UTR	Exon 1 of 5	NP_001096071.1	A0A0D9SF12
CCDC163	NM_001358407.2		c.-422C>A	5_prime_UTR	Exon 1 of 5	NP_001345336.1
CCDC163	NM_001358406.2		c.-422C>A	5_prime_UTR	Exon 1 of 6	NP_001345335.1	A0A0D9SG11

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CCDC163	ENST00000629482.3	TSL:1 MANE Select	c.-422C>A	5_prime_UTR	Exon 1 of 5	ENSP00000486197.1	A0A0D9SF12
CCDC163	ENST00000625766.2	TSL:1	n.-422C>A	non_coding_transcript_exon	Exon 1 of 5	ENSP00000486505.1	A0A0D9SFD8
CCDC163	ENST00000626177.2	TSL:1	n.-422C>A	non_coding_transcript_exon	Exon 1 of 6	ENSP00000485784.1	B4DV03

Frequencies

GnomAD3 genomes

AF:

0.738

AC:

112041

AN:

151912

Hom.:

41753

Cov.:

show subpopulations

Gnomad AFR

AF:

0.818

Gnomad AMI

AF:

0.762

Gnomad AMR

AF:

0.800

Gnomad ASJ

AF:

0.734

Gnomad EAS

AF:

0.942

Gnomad SAS

AF:

0.757

Gnomad FIN

AF:

0.678

Gnomad MID

AF:

0.756

Gnomad NFE

AF:

0.667

Gnomad OTH

AF:

0.735

GnomAD4 exome

AF:

0.711

AC:

260924

AN:

367190

Hom.:

94159

Cov.:

AF XY:

0.710

AC XY:

137491

AN XY:

193660

show subpopulations

African (AFR)

AF:

0.817

AC:

8828

AN:

10806

American (AMR)

AF:

0.844

AC:

13692

AN:

16228

Ashkenazi Jewish (ASJ)

AF:

0.731

AC:

8296

AN:

11348

East Asian (EAS)

AF:

0.950

AC:

22183

AN:

23342

South Asian (SAS)

AF:

0.733

AC:

31623

AN:

43162

European-Finnish (FIN)

AF:

0.675

AC:

14660

AN:

21720

Middle Eastern (MID)

AF:

0.757

AC:

1222

AN:

1614

European-Non Finnish (NFE)

AF:

0.667

AC:

145194

AN:

217706

Other (OTH)

AF:

0.716

AC:

15226

AN:

21264

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

3687

7374

11061

14748

18435

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

744

1488

2232

2976

3720

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.738

AC:

112131

AN:

152030

Hom.:

41787

Cov.:

AF XY:

0.742

AC XY:

55143

AN XY:

74310

show subpopulations

African (AFR)

AF:

0.818

AC:

33937

AN:

41496

American (AMR)

AF:

0.800

AC:

12224

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.734

AC:

2545

AN:

3468

East Asian (EAS)

AF:

0.942

AC:

4870

AN:

5170

South Asian (SAS)

AF:

0.757

AC:

3647

AN:

4818

European-Finnish (FIN)

AF:

0.678

AC:

7149

AN:

10544

Middle Eastern (MID)

AF:

0.762

AC:

224

AN:

294

European-Non Finnish (NFE)

AF:

0.667

AC:

45289

AN:

67944

Other (OTH)

AF:

0.737

AC:

1553

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1502

3005

4507

6010

7512

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

840

1680

2520

3360

4200

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.590

Hom.:

1749

Bravo

AF:

0.749

Asia WGS

AF:

0.857

AC:

2979

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

(source)

DANN

Benign

0.72

PhyloP100

0.68

PromoterAI

-0.052

Neutral

(source)

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over