11-4655747-G-T

Variant names:

• chr11-4655747-G-T
• rs7926081

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 0.419 in 151,860 control chromosomes in the GnomAD database, including 14,180 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 0.42 (14180 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.783

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 = 0.501 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: 0.419 AC: 63533 AN: 151740 Hom.: 14173 Cov.: 31

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.0412

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.419 AC: 63569 AN: 151860 Hom.: 14180 Cov.: 31 AF XY: 0.411 AC XY: 30514 AN XY: 74202

Gnomad4 AFR AF: 0.323

Gnomad4 AMR AF: 0.442

Gnomad4 ASJ AF: 0.480

Gnomad4 EAS AF: 0.0413

Gnomad4 SAS AF: 0.369

Gnomad4 FIN AF: 0.391

Gnomad4 NFE AF: 0.505

Gnomad4 OTH AF: 0.428

Alfa AF: 0.449 Hom.: 6741

Bravo AF: 0.413

Asia WGS AF: 0.214 AC: 749 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.8
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7926081; hg19: chr11-4676977;