rs972021

Variant names:

• chr2-83722614-A-G
• rs972021

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 0.962 in 151,982 control chromosomes in the GnomAD database, including 70,402 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 0.96 (70402 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.978 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: 0.962 AC: 146096 AN: 151864 Hom.: 70366 Cov.: 30

Gnomad AFR AF: 0.916

Gnomad AMI AF: 0.978

Gnomad AMR AF: 0.980

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.887

Gnomad FIN AF: 0.975

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.984

Gnomad OTH AF: 0.973

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

GnomAD4 genome AF: 0.962 AC: 146187 AN: 151982 Hom.: 70402 Cov.: 30 AF XY: 0.961 AC XY: 71384 AN XY: 74316

Gnomad4 AFR AF: 0.916

Gnomad4 AMR AF: 0.981

Gnomad4 ASJ AF: 1.00

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.887

Gnomad4 FIN AF: 0.975

Gnomad4 NFE AF: 0.984

Gnomad4 OTH AF: 0.970

Alfa AF: 0.977 Hom.: 22263

Bravo AF: 0.963

Asia WGS AF: 0.926 AC: 3220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.51
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs972021; hg19: chr2-83949738;