rs7926443

chr11-13144500-C-T

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 0.135 in 152,030 control chromosomes in the GnomAD database, including 1,569 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 0.13 (1569 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

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 (AFR) allele frequency at 95% confidence interval = 0.203 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: 0.135 AC: 20465 AN: 151910 Hom.: 1568 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.00366

Gnomad SAS AF: 0.0947

Gnomad FIN AF: 0.0824

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.135 AC: 20471 AN: 152030 Hom.: 1569 Cov.: 32 AF XY: 0.132 AC XY: 9816 AN XY: 74350

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.00367

Gnomad4 SAS AF: 0.0937

Gnomad4 FIN AF: 0.0824

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.150

Alfa AF: 0.122 Hom.: 2540

Bravo AF: 0.139

Asia WGS AF: 0.0600 AC: 209 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	0.38
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7926443; hg19: chr11-13166047;