rs62018380

Variant names:

• chr15-94732688-C-A
• rs62018380

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 0.125 in 151,096 control chromosomes in the GnomAD database, including 1,551 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 0.12 (1551 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.226 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: 0.125 AC: 18830 AN: 150974 Hom.: 1551 Cov.: 28

Gnomad AFR AF: 0.0366

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.0924

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.125 AC: 18829 AN: 151096 Hom.: 1551 Cov.: 28 AF XY: 0.129 AC XY: 9513 AN XY: 73738

African (AFR) AF: 0.0366 AC: 1504 AN: 41144

American (AMR) AF: 0.232 AC: 3522 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 421 AN: 3464

East Asian (EAS) AF: 0.128 AC: 646 AN: 5066

South Asian (SAS) AF: 0.236 AC: 1120 AN: 4736

European-Finnish (FIN) AF: 0.161 AC: 1677 AN: 10404

Middle Eastern (MID) AF: 0.0856 AC: 25 AN: 292

European-Non Finnish (NFE) AF: 0.139 AC: 9420 AN: 67804

Other (OTH) AF: 0.138 AC: 288 AN: 2092

Alfa AF: 0.125 Hom.: 191

Bravo AF: 0.127

Asia WGS AF: 0.168 AC: 583 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.2
DANN	Benign	0.40
PhyloP100		-0.046

Splicing

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

Other links and lift over

dbSNP: rs62018380; hg19: chr15-95275917;