rs7941534

Variant names:

• chr11-116529665-A-G
• rs7941534

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 0.193 in 152,110 control chromosomes in the GnomAD database, including 2,974 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 0.19 (2974 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.330
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.213 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: 0.193 AC: 29378 AN: 151992 Hom.: 2973 Cov.: 32

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.0331

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.193 AC: 29380 AN: 152110 Hom.: 2974 Cov.: 32 AF XY: 0.192 AC XY: 14268 AN XY: 74384

African (AFR) AF: 0.179 AC: 7432 AN: 41476

American (AMR) AF: 0.195 AC: 2986 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 936 AN: 3468

East Asian (EAS) AF: 0.0330 AC: 171 AN: 5184

South Asian (SAS) AF: 0.189 AC: 909 AN: 4820

European-Finnish (FIN) AF: 0.140 AC: 1480 AN: 10586

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.215 AC: 14649 AN: 67986

Other (OTH) AF: 0.225 AC: 475 AN: 2108

Alfa AF: 0.208 Hom.: 10943

Bravo AF: 0.192

Asia WGS AF: 0.113 AC: 395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.51
DANN	Benign	0.50
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs7941534; hg19: chr11-116400382;