5-157983270-A-T

Variant names:

• chr5-157983270-A-T
• rs11958404

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 0.125 in 152,058 control chromosomes in the GnomAD database, including 1,401 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 0.12 (1401 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.602
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.125 AC: 18981 AN: 151940 Hom.: 1397 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.0866

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.0977

Gnomad FIN AF: 0.0742

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.125 AC: 19002 AN: 152058 Hom.: 1401 Cov.: 32 AF XY: 0.122 AC XY: 9100 AN XY: 74356

African (AFR) AF: 0.195 AC: 8087 AN: 41452

American (AMR) AF: 0.0865 AC: 1321 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 438 AN: 3468

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5184

South Asian (SAS) AF: 0.0972 AC: 469 AN: 4826

European-Finnish (FIN) AF: 0.0742 AC: 783 AN: 10556

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7527 AN: 67980

Other (OTH) AF: 0.112 AC: 236 AN: 2116

Alfa AF: 0.0356 Hom.: 44

Bravo AF: 0.128

Asia WGS AF: 0.0620 AC: 219 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.56
DANN	Benign	0.62
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs11958404; hg19: chr5-157410278;