chr11-102734848-A-G

Position:

• chr11-102734848-A-G

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 0.546 in 152,120 control chromosomes in the GnomAD database, including 22,987 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 0.55 (22987 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.102

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 (NFE) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.546 AC: 82957 AN: 152004 Hom.: 22981 Cov.: 33

Gnomad AFR AF: 0.543

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.546 AC: 82990 AN: 152120 Hom.: 22987 Cov.: 33 AF XY: 0.542 AC XY: 40260 AN XY: 74328

Gnomad4 AFR AF: 0.542

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.616

Gnomad4 EAS AF: 0.247

Gnomad4 SAS AF: 0.461

Gnomad4 FIN AF: 0.569

Gnomad4 NFE AF: 0.582

Gnomad4 OTH AF: 0.558

Alfa AF: 0.573 Hom.: 50424

Bravo AF: 0.542

Asia WGS AF: 0.362 AC: 1259 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	2.8
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10791591; hg19: chr11-102605579;