11-76567214-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 0.583 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;