dbSNP rs9806234: ENSG00000261821:n.4498A>G (chr15-74370692-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000568496.3(ENSG00000261821):n.4498A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 152,072 control chromosomes in the GnomAD database, including 15,534 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 0.41 ( 15532 hom., cov: 32)

Exomes 𝑓: 0.50 ( 2 hom. )

Consequence

ENSG00000261821
ENST00000568496.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.92

Publications

11 publications found

Variant links:

Genes affected

ENSG00000261821 (HGNC:):

ENSG00000261821 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=-1.0).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903524	XR_007064709.1 link	n.5075A>G		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000261821	ENST00000568496.3 link	n.4498A>G	non_coding_transcript_exon_variant	Exon 3 of 3	2
ENSG00000261821	ENST00000783990.1 link	n.689A>G	non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000261821	ENST00000783991.1 link	n.764A>G	non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.407

AC:

61819

AN:

151942

Hom.:

15496

Cov.:

show subpopulations

Gnomad AFR

AF:

0.683

Gnomad AMI

AF:

0.418

Gnomad AMR

AF:

0.322

Gnomad ASJ

AF:

0.343

Gnomad EAS

AF:

0.648

Gnomad SAS

AF:

0.609

Gnomad FIN

AF:

0.250

Gnomad MID

AF:

0.440

Gnomad NFE

AF:

0.253

Gnomad OTH

AF:

0.384

GnomAD4 exome

AF:

0.500

AC:

AN:

Hom.:

Cov.:

AF XY:

0.833

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AF:

0.500

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

Age Distribution

Exome Hom

Variant carriers

<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:

0.407

AC:

61922

AN:

152060

Hom.:

15532

Cov.:

AF XY:

0.412

AC XY:

30591

AN XY:

74324

show subpopulations

African (AFR)

AF:

0.683

AC:

28304

AN:

41452

American (AMR)

AF:

0.323

AC:

4935

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.343

AC:

1191

AN:

3468

East Asian (EAS)

AF:

0.648

AC:

3345

AN:

5160

South Asian (SAS)

AF:

0.610

AC:

2941

AN:

4824

European-Finnish (FIN)

AF:

0.250

AC:

2646

AN:

10580

Middle Eastern (MID)

AF:

0.446

AC:

131

AN:

294

European-Non Finnish (NFE)

AF:

0.253

AC:

17231

AN:

67978

Other (OTH)

AF:

0.388

AC:

818

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1604

3207

4811

6414

8018

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

552

1104

1656

2208

2760

<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:

0.306

Hom.:

10456

Bravo

AF:

0.422

Asia WGS

AF:

0.639

AC:

2222

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.46

(source)

DANN

Benign

0.18

PhyloP100

-1.9

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over