rs4756763

Positions:

• chr11-13259009-G-A
• chr11-13259009-G-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 0.473 in 151,994 control chromosomes in the GnomAD database, including 18,015 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 0.47 (18015 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.566 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.473 AC: 71804 AN: 151876 Hom.: 18002 Cov.: 31

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.473 AC: 71867 AN: 151994 Hom.: 18015 Cov.: 31 AF XY: 0.470 AC XY: 34921 AN XY: 74264

Gnomad4 AFR AF: 0.320

Gnomad4 AMR AF: 0.486

Gnomad4 ASJ AF: 0.522

Gnomad4 EAS AF: 0.273

Gnomad4 SAS AF: 0.454

Gnomad4 FIN AF: 0.522

Gnomad4 NFE AF: 0.570

Gnomad4 OTH AF: 0.501

Alfa AF: 0.556 Hom.: 45508

Bravo AF: 0.465

Asia WGS AF: 0.380 AC: 1320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4756763; hg19: chr11-13280556;