chr11-102516960-C-T

Position:

• chr11-102516960-C-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 0.0805 in 152,238 control chromosomes in the GnomAD database, including 494 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 0.081 (494 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0997 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: 0.0804 AC: 12224 AN: 152120 Hom.: 490 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0745

Gnomad ASJ AF: 0.0727

Gnomad EAS AF: 0.0144

Gnomad SAS AF: 0.0424

Gnomad FIN AF: 0.0509

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0824

Gnomad OTH AF: 0.0765

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

GnomAD4 genome AF: 0.0805 AC: 12259 AN: 152238 Hom.: 494 Cov.: 32 AF XY: 0.0778 AC XY: 5792 AN XY: 74432

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.0745

Gnomad4 ASJ AF: 0.0727

Gnomad4 EAS AF: 0.0145

Gnomad4 SAS AF: 0.0431

Gnomad4 FIN AF: 0.0509

Gnomad4 NFE AF: 0.0824

Gnomad4 OTH AF: 0.0762

Alfa AF: 0.0898 Hom.: 123

Bravo AF: 0.0830

Asia WGS AF: 0.0290 AC: 101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.65
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17098236; hg19: chr11-102387691;