2-85938320-T-C

Variant names:

• chr2-85938320-T-C
• rs11691934

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 0.633 in 151,978 control chromosomes in the GnomAD database, including 30,594 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 (30594 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.695 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: 0.633 AC: 96180 AN: 151860 Hom.: 30575 Cov.: 31

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.715

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.633 AC: 96246 AN: 151978 Hom.: 30594 Cov.: 31 AF XY: 0.635 AC XY: 47155 AN XY: 74288

Gnomad4 AFR AF: 0.593

Gnomad4 AMR AF: 0.684

Gnomad4 ASJ AF: 0.603

Gnomad4 EAS AF: 0.715

Gnomad4 SAS AF: 0.652

Gnomad4 FIN AF: 0.658

Gnomad4 NFE AF: 0.637

Gnomad4 OTH AF: 0.637

Alfa AF: 0.637 Hom.: 64259

Bravo AF: 0.638

Asia WGS AF: 0.645 AC: 2242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.017
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11691934; hg19: chr2-86165443;