chr11-76256419-G-A

Position:

• chr11-76256419-G-A

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 0.503 in 141,790 control chromosomes in the GnomAD database, including 18,605 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 0.50 (18605 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.898

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.504 AC: 71386 AN: 141700 Hom.: 18611 Cov.: 24

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.540

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.648

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.503 AC: 71381 AN: 141790 Hom.: 18605 Cov.: 24 AF XY: 0.496 AC XY: 34078 AN XY: 68678

Gnomad4 AFR AF: 0.323

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.637

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.403

Gnomad4 FIN AF: 0.514

Gnomad4 NFE AF: 0.623

Gnomad4 OTH AF: 0.534

Alfa AF: 0.527 Hom.: 2398

Bravo AF: 0.477

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.5
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7104908; hg19: chr11-75967463;