chr15-62102491-C-G

Variant names:

• chr15-62102491-C-G
• rs6494307

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.481 in 152,020 control chromosomes in the GnomAD database, including 18,153 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 0.48 (18153 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.999
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.595 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.481 AC: 73048 AN: 151902 Hom.: 18104 Cov.: 32

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.414

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.477

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.481 AC: 73164 AN: 152020 Hom.: 18153 Cov.: 32 AF XY: 0.483 AC XY: 35907 AN XY: 74288

African (AFR) AF: 0.601 AC: 24939 AN: 41472

American (AMR) AF: 0.465 AC: 7109 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1177 AN: 3466

East Asian (EAS) AF: 0.363 AC: 1878 AN: 5174

South Asian (SAS) AF: 0.382 AC: 1839 AN: 4816

European-Finnish (FIN) AF: 0.555 AC: 5844 AN: 10530

Middle Eastern (MID) AF: 0.428 AC: 125 AN: 292

European-Non Finnish (NFE) AF: 0.423 AC: 28779 AN: 67972

Other (OTH) AF: 0.477 AC: 1008 AN: 2114

Alfa AF: 0.463 Hom.: 2080

Bravo AF: 0.480

Asia WGS AF: 0.437 AC: 1519 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.068
DANN	Benign	0.45
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs6494307; hg19: chr15-62394690;