rs1562308

chr2-61541286-A-Cchr2-61541286-A-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 0.631 in 151,476 control chromosomes in the GnomAD database, including 30,353 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 0.63 (30353 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.475

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 (AFR) allele frequency at 95% confidence interval = 0.679 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: 0.631 AC: 95493 AN: 151358 Hom.: 30313 Cov.: 29

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.655

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

GnomAD4 genome AF: 0.631 AC: 95588 AN: 151476 Hom.: 30353 Cov.: 29 AF XY: 0.631 AC XY: 46670 AN XY: 73986

Gnomad4 AFR AF: 0.686

Gnomad4 AMR AF: 0.586

Gnomad4 ASJ AF: 0.673

Gnomad4 EAS AF: 0.649

Gnomad4 SAS AF: 0.612

Gnomad4 FIN AF: 0.601

Gnomad4 NFE AF: 0.608

Gnomad4 OTH AF: 0.653

Alfa AF: 0.515 Hom.: 1857

Bravo AF: 0.633

Asia WGS AF: 0.625 AC: 2175 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	0.97
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1562308; hg19: chr2-61768421;