rs7102746

Variant names:

• chr11-92933397-T-C
• rs7102746

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;