rs7102746

Positions:

• chr11-92933397-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 0.637 in 152,062 control chromosomes in the GnomAD database, including 33,075 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 0.64 (33075 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.898 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: 0.637 AC: 96801 AN: 151944 Hom.: 33026 Cov.: 32

Gnomad AFR AF: 0.906

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.637 AC: 96908 AN: 152062 Hom.: 33075 Cov.: 32 AF XY: 0.635 AC XY: 47169 AN XY: 74324

Gnomad4 AFR AF: 0.906

Gnomad4 AMR AF: 0.586

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.556

Gnomad4 SAS AF: 0.506

Gnomad4 FIN AF: 0.521

Gnomad4 NFE AF: 0.530

Gnomad4 OTH AF: 0.597

Alfa AF: 0.571 Hom.: 7425

Bravo AF: 0.654

Asia WGS AF: 0.525 AC: 1828 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.60
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: rs7102746; hg19: chr11-92666563;