chr5-138469963-G-T

Variant names:

• chr5-138469963-G-T
• rs11741807

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 0.545 in 152,104 control chromosomes in the GnomAD database, including 23,473 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 0.55 (23473 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82833 AN: 151984 Hom.: 23440 Cov.: 33

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.449

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.545 AC: 82920 AN: 152104 Hom.: 23473 Cov.: 33 AF XY: 0.543 AC XY: 40330 AN XY: 74338

African (AFR) AF: 0.483 AC: 20025 AN: 41486

American (AMR) AF: 0.575 AC: 8772 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.598 AC: 2075 AN: 3470

East Asian (EAS) AF: 0.177 AC: 914 AN: 5174

South Asian (SAS) AF: 0.369 AC: 1780 AN: 4822

European-Finnish (FIN) AF: 0.668 AC: 7069 AN: 10584

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.597 AC: 40573 AN: 67988

Other (OTH) AF: 0.548 AC: 1155 AN: 2108

Alfa AF: 0.579 Hom.: 45207

Bravo AF: 0.535

Asia WGS AF: 0.306 AC: 1064 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.8
DANN	Benign	0.69
PhyloP100		-0.068

Splicing

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

Other links and lift over

dbSNP: rs11741807; hg19: chr5-137805652;