rs973968

Variant names:

• chr14-62187980-G-A
• rs973968

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 0.821 in 151,856 control chromosomes in the GnomAD database, including 51,573 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 0.82 (51573 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0750
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.916 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: 0.822 AC: 124666 AN: 151740 Hom.: 51546 Cov.: 32

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.930

Gnomad AMR AF: 0.830

Gnomad ASJ AF: 0.898

Gnomad EAS AF: 0.938

Gnomad SAS AF: 0.889

Gnomad FIN AF: 0.868

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.837

Gnomad OTH AF: 0.841

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

GnomAD4 genome AF: 0.821 AC: 124742 AN: 151856 Hom.: 51573 Cov.: 32 AF XY: 0.826 AC XY: 61311 AN XY: 74246

African (AFR) AF: 0.748 AC: 30871 AN: 41286

American (AMR) AF: 0.830 AC: 12656 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.898 AC: 3117 AN: 3470

East Asian (EAS) AF: 0.938 AC: 4822 AN: 5140

South Asian (SAS) AF: 0.889 AC: 4292 AN: 4828

European-Finnish (FIN) AF: 0.868 AC: 9196 AN: 10596

Middle Eastern (MID) AF: 0.939 AC: 276 AN: 294

European-Non Finnish (NFE) AF: 0.837 AC: 56885 AN: 67976

Other (OTH) AF: 0.842 AC: 1779 AN: 2112

Alfa AF: 0.838 Hom.: 251838

Bravo AF: 0.818

Asia WGS AF: 0.875 AC: 3043 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.15
DANN	Benign	0.47
PhyloP100		-0.075

Splicing

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

Other links and lift over

dbSNP: rs973968; hg19: chr14-62654698;