rs7129386

Variant names:

• chr11-48595142-A-G
• rs7129386

Your query was ambiguous. Multiple possible variants found:

• chr11-48595142-A-G
• chr11-48595142-A-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 0.537 in 151,880 control chromosomes in the GnomAD database, including 23,320 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 0.54 (23320 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.62 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: 0.537 AC: 81472 AN: 151762 Hom.: 23298 Cov.: 32

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.604

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.537 AC: 81541 AN: 151880 Hom.: 23320 Cov.: 32 AF XY: 0.537 AC XY: 39818 AN XY: 74206

African (AFR) AF: 0.344 AC: 14250 AN: 41452

American (AMR) AF: 0.604 AC: 9198 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.617 AC: 2139 AN: 3466

East Asian (EAS) AF: 0.458 AC: 2351 AN: 5136

South Asian (SAS) AF: 0.420 AC: 2014 AN: 4798

European-Finnish (FIN) AF: 0.673 AC: 7095 AN: 10542

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.625 AC: 42445 AN: 67944

Other (OTH) AF: 0.559 AC: 1177 AN: 2106

Alfa AF: 0.571 Hom.: 11435

Bravo AF: 0.529

Asia WGS AF: 0.426 AC: 1483 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.1
DANN	Benign	0.79
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs7129386; hg19: chr11-48616694;