rs2980976

Variant names:

• chr18-62412879-G-A
• rs2980976

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.227

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.0889

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.195

Alfa AF: 0.166 Hom.: 1217

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2980976; hg19: chr18-60080112;