rs11247946

Variant names:

• chr1-26392624-T-C
• rs11247946

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.323 in 151,886 control chromosomes in the GnomAD database, including 8,640 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 0.32 (8640 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0690
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.638 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: 0.323 AC: 48988 AN: 151768 Hom.: 8630 Cov.: 29

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.323 AC: 49013 AN: 151886 Hom.: 8640 Cov.: 29 AF XY: 0.328 AC XY: 24376 AN XY: 74254

African (AFR) AF: 0.198 AC: 8217 AN: 41398

American (AMR) AF: 0.354 AC: 5398 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1140 AN: 3462

East Asian (EAS) AF: 0.656 AC: 3378 AN: 5146

South Asian (SAS) AF: 0.386 AC: 1858 AN: 4812

European-Finnish (FIN) AF: 0.437 AC: 4617 AN: 10568

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.341 AC: 23190 AN: 67948

Other (OTH) AF: 0.346 AC: 728 AN: 2106

Alfa AF: 0.339 Hom.: 29350

Bravo AF: 0.317

Asia WGS AF: 0.557 AC: 1933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.21
PhyloP100		0.069

Splicing

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

Other links and lift over

dbSNP: rs11247946; hg19: chr1-26719115; COSMIC: COSV59932931;