11-76567214-T-C

Variant names:

• chr11-76567214-T-C
• rs7936562

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 0.583 in 152,120 control chromosomes in the GnomAD database, including 26,089 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 0.58 (26089 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.863

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.607 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: 0.583 AC: 88678 AN: 152002 Hom.: 26076 Cov.: 32

Gnomad AFR AF: 0.614

Gnomad AMI AF: 0.717

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.583 AC: 88732 AN: 152120 Hom.: 26089 Cov.: 32 AF XY: 0.579 AC XY: 43098 AN XY: 74376

Gnomad4 AFR AF: 0.614

Gnomad4 AMR AF: 0.511

Gnomad4 ASJ AF: 0.699

Gnomad4 EAS AF: 0.531

Gnomad4 SAS AF: 0.500

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.585

Gnomad4 OTH AF: 0.585

Alfa AF: 0.583 Hom.: 52370

Bravo AF: 0.583

Asia WGS AF: 0.493 AC: 1715 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.35
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7936562; hg19: chr11-76278258;