rs6494311

Variant names:

• chr15-62135165-C-T
• rs6494311

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 0.378 in 152,128 control chromosomes in the GnomAD database, including 11,064 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 0.38 (11064 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.107
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.416 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: 0.378 AC: 57485 AN: 152010 Hom.: 11046 Cov.: 33

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.378 AC: 57535 AN: 152128 Hom.: 11064 Cov.: 33 AF XY: 0.377 AC XY: 28034 AN XY: 74360

African (AFR) AF: 0.312 AC: 12931 AN: 41506

American (AMR) AF: 0.422 AC: 6457 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1209 AN: 3470

East Asian (EAS) AF: 0.226 AC: 1171 AN: 5182

South Asian (SAS) AF: 0.350 AC: 1686 AN: 4818

European-Finnish (FIN) AF: 0.381 AC: 4029 AN: 10576

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.420 AC: 28520 AN: 67964

Other (OTH) AF: 0.408 AC: 863 AN: 2116

Alfa AF: 0.406 Hom.: 54010

Bravo AF: 0.376

Asia WGS AF: 0.321 AC: 1118 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.50
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs6494311; hg19: chr15-62427364;