rs11129795

Variant names:

• chr3-38547672-G-A
• rs11129795

Your query was ambiguous. Multiple possible variants found:

• chr3-38547672-G-A
• chr3-38547672-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 0.211 in 151,980 control chromosomes in the GnomAD database, including 3,441 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 0.21 (3441 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.261
• Publications: 45 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 (NFE) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32039 AN: 151860 Hom.: 3438 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.0978

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.211 AC: 32055 AN: 151980 Hom.: 3441 Cov.: 32 AF XY: 0.211 AC XY: 15639 AN XY: 74288

African (AFR) AF: 0.183 AC: 7572 AN: 41434

American (AMR) AF: 0.186 AC: 2848 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 759 AN: 3470

East Asian (EAS) AF: 0.0982 AC: 509 AN: 5182

South Asian (SAS) AF: 0.168 AC: 806 AN: 4804

European-Finnish (FIN) AF: 0.281 AC: 2966 AN: 10556

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15760 AN: 67944

Other (OTH) AF: 0.206 AC: 436 AN: 2114

Alfa AF: 0.228 Hom.: 16714

Bravo AF: 0.206

Asia WGS AF: 0.145 AC: 508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.15
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs11129795; hg19: chr3-38589163;