rs981525

chr2-83432543-G-Achr2-83432543-G-Cchr2-83432543-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 0.457 in 151,948 control chromosomes in the GnomAD database, including 16,463 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 0.46 (16463 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68

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 = 0.806 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: 0.457 AC: 69324 AN: 151830 Hom.: 16445 Cov.: 32

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.457 AC: 69388 AN: 151948 Hom.: 16463 Cov.: 32 AF XY: 0.460 AC XY: 34139 AN XY: 74278

Gnomad4 AFR AF: 0.427

Gnomad4 AMR AF: 0.570

Gnomad4 ASJ AF: 0.414

Gnomad4 EAS AF: 0.827

Gnomad4 SAS AF: 0.434

Gnomad4 FIN AF: 0.407

Gnomad4 NFE AF: 0.431

Gnomad4 OTH AF: 0.476

Alfa AF: 0.448 Hom.: 14061

Bravo AF: 0.474

Asia WGS AF: 0.643 AC: 2232 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.079
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs981525; hg19: chr2-83659667;