rs7106715

Variant names:

• chr11-133969010-C-T
• rs7106715

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 0.158 in 152,254 control chromosomes in the GnomAD database, including 2,495 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 0.16 (2495 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.331

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.216 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: 0.158 AC: 24061 AN: 152136 Hom.: 2496 Cov.: 33

Gnomad AFR AF: 0.0473

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.0438

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.158 AC: 24061 AN: 152254 Hom.: 2495 Cov.: 33 AF XY: 0.159 AC XY: 11833 AN XY: 74434

Gnomad4 AFR AF: 0.0473

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.0438

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.136

Alfa AF: 0.186 Hom.: 547

Bravo AF: 0.139

Asia WGS AF: 0.0630 AC: 219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.0
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7106715; hg19: chr11-133838905;