rs973968

chr14-62187980-G-A

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 0.821 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.748

Gnomad4 AMR AF: 0.830

Gnomad4 ASJ AF: 0.898

Gnomad4 EAS AF: 0.938

Gnomad4 SAS AF: 0.889

Gnomad4 FIN AF: 0.868

Gnomad4 NFE AF: 0.837

Gnomad4 OTH AF: 0.842

Alfa AF: 0.845 Hom.: 123467

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs973968; hg19: chr14-62654698;