Genetic Variant RCCD1:c.-172T>C (chr15-90954900-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001017919.2(RCCD1):c.-172T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 152,074 control chromosomes in the GnomAD database, including 6,888 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.29 ( 6885 hom., cov: 33)

Exomes 𝑓: 0.29 ( 3 hom. )

Consequence

RCCD1
NM_001017919.2 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.18

Publications

11 publications found

Variant links:

Genes affected

RCCD1 (HGNC:30457): (RCC1 domain containing 1) Predicted to be involved in chromatin organization. Located in cytosol and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

RCCD1 links:

RCCD1-AS1 (HGNC:54811): (RCCD1 and UNC45A antisense RNA 1)

RCCD1-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001017919.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RCCD1	NM_001017919.2	MANE Select	c.-172T>C		5_prime_UTR	Exon 1 of 8	NP_001017919.1	A6NED2
	RCCD1	NM_033544.3		c.-256T>C		5_prime_UTR	Exon 1 of 9	NP_291022.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
RCCD1	ENST00000394258.7	TSL:1 MANE Select	c.-172T>C	5_prime_UTR	Exon 1 of 8	ENSP00000377801.2	A6NED2
RCCD1	ENST00000555737.5	TSL:1	n.17T>C	non_coding_transcript_exon	Exon 1 of 6
RCCD1	ENST00000852981.1		c.-256T>C	5_prime_UTR	Exon 1 of 9	ENSP00000523040.1

Frequencies

GnomAD3 genomes

AF:

0.294

AC:

44620

AN:

151864

Hom.:

6867

Cov.:

show subpopulations

Gnomad AFR

AF:

0.323

Gnomad AMI

AF:

0.160

Gnomad AMR

AF:

0.345

Gnomad ASJ

AF:

0.189

Gnomad EAS

AF:

0.557

Gnomad SAS

AF:

0.239

Gnomad FIN

AF:

0.284

Gnomad MID

AF:

0.274

Gnomad NFE

AF:

0.257

Gnomad OTH

AF:

0.295

GnomAD4 exome

AF:

0.289

AC:

AN:

Hom.:

Cov.:

AF XY:

0.300

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.750

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.250

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.289

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.294

AC:

44678

AN:

151984

Hom.:

6885

Cov.:

AF XY:

0.298

AC XY:

22108

AN XY:

74312

show subpopulations

African (AFR)

AF:

0.323

AC:

13395

AN:

41476

American (AMR)

AF:

0.346

AC:

5288

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.189

AC:

656

AN:

3464

East Asian (EAS)

AF:

0.556

AC:

2846

AN:

5118

South Asian (SAS)

AF:

0.238

AC:

1149

AN:

4824

European-Finnish (FIN)

AF:

0.284

AC:

3008

AN:

10576

Middle Eastern (MID)

AF:

0.288

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.257

AC:

17476

AN:

67928

Other (OTH)

AF:

0.299

AC:

630

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

1603

3206

4810

6413

8016

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

458

916

1374

1832

2290

<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:

0.185

Hom.:

625

Bravo

AF:

0.305

Asia WGS

AF:

0.422

AC:

1463

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

0.17

(source)

DANN

Benign

0.35

PhyloP100

-2.2

PromoterAI

-0.056

Neutral

(source)

Mutation Taster

=300/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over