rs962528

chr2-6556956-C-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 0.264 in 151,824 control chromosomes in the GnomAD database, including 6,139 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 0.26 (6139 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.421 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: 0.264 AC: 40048 AN: 151706 Hom.: 6133 Cov.: 31

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.240

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.264 AC: 40063 AN: 151824 Hom.: 6139 Cov.: 31 AF XY: 0.268 AC XY: 19898 AN XY: 74196

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.436

Gnomad4 SAS AF: 0.372

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.265

Alfa AF: 0.299 Hom.: 4121

Bravo AF: 0.248

Asia WGS AF: 0.407 AC: 1413 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	3.3
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs962528; hg19: chr2-6697088;