rs983970

Positions:

• chr2-125383270-G-A
• chr2-125383270-G-T

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 0.483 in 149,568 control chromosomes in the GnomAD database, including 18,314 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 0.48 (18314 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.483 AC: 72136 AN: 149478 Hom.: 18300 Cov.: 28

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.625

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.483 AC: 72189 AN: 149568 Hom.: 18314 Cov.: 28 AF XY: 0.490 AC XY: 35659 AN XY: 72734

Gnomad4 AFR AF: 0.354

Gnomad4 AMR AF: 0.575

Gnomad4 ASJ AF: 0.577

Gnomad4 EAS AF: 0.864

Gnomad4 SAS AF: 0.624

Gnomad4 FIN AF: 0.497

Gnomad4 NFE AF: 0.493

Gnomad4 OTH AF: 0.533

Alfa AF: 0.499 Hom.: 3287

Bravo AF: 0.481

Asia WGS AF: 0.736 AC: 2555 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.12
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs983970; hg19: chr2-126140847;