chr5-157009668-T-A

Variant names:

• chr5-157009668-T-A
• rs1995377

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 0.88 in 152,138 control chromosomes in the GnomAD database, including 58,968 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 0.88 (58968 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.965 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: 0.880 AC: 133702 AN: 152020 Hom.: 58906 Cov.: 30

Gnomad AFR AF: 0.913

Gnomad AMI AF: 0.984

Gnomad AMR AF: 0.916

Gnomad ASJ AF: 0.915

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.949

Gnomad FIN AF: 0.855

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.838

Gnomad OTH AF: 0.885

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

GnomAD4 genome AF: 0.880 AC: 133822 AN: 152138 Hom.: 58968 Cov.: 30 AF XY: 0.883 AC XY: 65687 AN XY: 74370

African (AFR) AF: 0.913 AC: 37908 AN: 41520

American (AMR) AF: 0.916 AC: 13997 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.915 AC: 3177 AN: 3472

East Asian (EAS) AF: 0.987 AC: 5115 AN: 5180

South Asian (SAS) AF: 0.949 AC: 4570 AN: 4816

European-Finnish (FIN) AF: 0.855 AC: 9031 AN: 10560

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.838 AC: 56995 AN: 67990

Other (OTH) AF: 0.887 AC: 1877 AN: 2116

Alfa AF: 0.852 Hom.: 6877

Bravo AF: 0.886

Asia WGS AF: 0.960 AC: 3338 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.65
DANN	Benign	0.21
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1995377; hg19: chr5-156436679;