11-102534940-A-T

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 0.799 in 152,154 control chromosomes in the GnomAD database, including 49,065 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 0.80 (49065 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.234

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.886 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: 0.799 AC: 121495 AN: 152034 Hom.: 49005 Cov.: 31

Gnomad AFR AF: 0.893

Gnomad AMI AF: 0.851

Gnomad AMR AF: 0.725

Gnomad ASJ AF: 0.821

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.737

Gnomad FIN AF: 0.755

Gnomad MID AF: 0.876

Gnomad NFE AF: 0.782

Gnomad OTH AF: 0.802

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

GnomAD4 genome AF: 0.799 AC: 121617 AN: 152154 Hom.: 49065 Cov.: 31 AF XY: 0.795 AC XY: 59160 AN XY: 74396

Gnomad4 AFR AF: 0.894

Gnomad4 AMR AF: 0.726

Gnomad4 ASJ AF: 0.821

Gnomad4 EAS AF: 0.609

Gnomad4 SAS AF: 0.737

Gnomad4 FIN AF: 0.755

Gnomad4 NFE AF: 0.782

Gnomad4 OTH AF: 0.800

Alfa AF: 0.796 Hom.: 6000

Bravo AF: 0.802

Asia WGS AF: 0.709 AC: 2468 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.77
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs880197; hg19: chr11-102405671;