rs11247946

Positions:

• chr1-26392624-T-C

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 0.323 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0690

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.26392624T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.354

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.656

Gnomad4 SAS AF: 0.386

Gnomad4 FIN AF: 0.437

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.346

Alfa AF: 0.339 Hom.: 12201

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

Splicing

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

Publications

LitVar

Other links and lift over

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