rs11762043

Variant names:

• chr7-154909941-G-A
• rs11762043

Your query was ambiguous. Multiple possible variants found:

• chr7-154909941-G-A
• chr7-154909941-G-T

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 0.13 in 152,246 control chromosomes in the GnomAD database, including 1,356 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 (1356 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.157 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: 0.130 AC: 19824 AN: 152128 Hom.: 1355 Cov.: 33

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.0956

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.0440

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.0956

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.130 AC: 19849 AN: 152246 Hom.: 1356 Cov.: 33 AF XY: 0.128 AC XY: 9557 AN XY: 74450

African (AFR) AF: 0.159 AC: 6605 AN: 41538

American (AMR) AF: 0.0954 AC: 1460 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 436 AN: 3470

East Asian (EAS) AF: 0.0441 AC: 228 AN: 5174

South Asian (SAS) AF: 0.167 AC: 806 AN: 4830

European-Finnish (FIN) AF: 0.0956 AC: 1015 AN: 10616

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.131 AC: 8917 AN: 67998

Other (OTH) AF: 0.136 AC: 287 AN: 2112

Alfa AF: 0.115 Hom.: 591

Bravo AF: 0.130

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.71
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs11762043; hg19: chr7-154701651;