rs2980976

Variant names:

• chr18-62412879-G-A
• rs2980976

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 0.174 in 152,162 control chromosomes in the GnomAD database, including 2,541 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 0.17 (2541 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.175
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.396 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: 0.174 AC: 26408 AN: 152044 Hom.: 2544 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.0889

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.174 AC: 26403 AN: 152162 Hom.: 2541 Cov.: 32 AF XY: 0.175 AC XY: 12989 AN XY: 74382

African (AFR) AF: 0.211 AC: 8765 AN: 41500

American (AMR) AF: 0.159 AC: 2430 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 816 AN: 3468

East Asian (EAS) AF: 0.227 AC: 1174 AN: 5176

South Asian (SAS) AF: 0.411 AC: 1984 AN: 4824

European-Finnish (FIN) AF: 0.0889 AC: 942 AN: 10598

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9624 AN: 67988

Other (OTH) AF: 0.195 AC: 411 AN: 2108

Alfa AF: 0.159 Hom.: 4251

Bravo AF: 0.176

Asia WGS AF: 0.264 AC: 916 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.9
DANN	Benign	0.45
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs2980976; hg19: chr18-60080112;