rs7926443

Variant names:

• chr11-13144500-C-T
• rs7926443

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.207 AC: 8577 AN: 41414

American (AMR) AF: 0.110 AC: 1685 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 553 AN: 3472

East Asian (EAS) AF: 0.00367 AC: 19 AN: 5180

South Asian (SAS) AF: 0.0937 AC: 452 AN: 4824

European-Finnish (FIN) AF: 0.0824 AC: 871 AN: 10576

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.115 AC: 7803 AN: 67984

Other (OTH) AF: 0.150 AC: 317 AN: 2110

Alfa AF: 0.127 Hom.: 4189

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
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs7926443; hg19: chr11-13166047;