5-139332497-T-A

Variant names:

• chr5-139332497-T-A
• rs11738738

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 0.511 in 152,046 control chromosomes in the GnomAD database, including 24,131 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 0.51 (24131 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 2 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 = 0.692 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: 0.511 AC: 77622 AN: 151928 Hom.: 24134 Cov.: 31

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.511 AC: 77622 AN: 152046 Hom.: 24131 Cov.: 31 AF XY: 0.506 AC XY: 37604 AN XY: 74304

African (AFR) AF: 0.161 AC: 6674 AN: 41524

American (AMR) AF: 0.573 AC: 8743 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.689 AC: 2391 AN: 3472

East Asian (EAS) AF: 0.197 AC: 1018 AN: 5164

South Asian (SAS) AF: 0.621 AC: 2996 AN: 4822

European-Finnish (FIN) AF: 0.621 AC: 6554 AN: 10554

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.697 AC: 47387 AN: 67944

Other (OTH) AF: 0.546 AC: 1154 AN: 2112

Alfa AF: 0.497 Hom.: 1795

Bravo AF: 0.490

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.55
DANN	Benign	0.53
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs11738738; hg19: chr5-138668186;