11-111326133-T-C

Variant names:

• chr11-111326133-T-C
• rs7104791

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 0.743 in 151,940 control chromosomes in the GnomAD database, including 42,541 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 0.74 (42541 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106

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 (AMR) allele frequency at 95% confidence interval = 0.804 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: 0.743 AC: 112792 AN: 151822 Hom.: 42523 Cov.: 31

Gnomad AFR AF: 0.719

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.817

Gnomad ASJ AF: 0.800

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.704

Gnomad MID AF: 0.809

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.785

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

GnomAD4 genome AF: 0.743 AC: 112867 AN: 151940 Hom.: 42541 Cov.: 31 AF XY: 0.735 AC XY: 54616 AN XY: 74272

Gnomad4 AFR AF: 0.719

Gnomad4 AMR AF: 0.816

Gnomad4 ASJ AF: 0.800

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.532

Gnomad4 FIN AF: 0.704

Gnomad4 NFE AF: 0.781

Gnomad4 OTH AF: 0.782

Alfa AF: 0.773 Hom.: 91789

Bravo AF: 0.753

Asia WGS AF: 0.460 AC: 1602 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	4.8
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7104791; hg19: chr11-111196858;