rs981525

Variant names:

• chr2-83432543-G-A
• rs981525

Your query was ambiguous. Multiple possible variants found:

• chr2-83432543-G-A
• chr2-83432543-G-C
• chr2-83432543-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;