chr5-156971242-G-A

Variant names:

• chr5-156971242-G-A
• rs6883317

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 0.173 in 152,170 control chromosomes in the GnomAD database, including 2,340 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 0.17 (2340 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410
• Publications: 4 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 (AFR) allele frequency at 95% confidence interval = 0.193 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: 0.173 AC: 26241 AN: 152052 Hom.: 2344 Cov.: 33

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.173 AC: 26252 AN: 152170 Hom.: 2340 Cov.: 33 AF XY: 0.171 AC XY: 12704 AN XY: 74410

African (AFR) AF: 0.196 AC: 8153 AN: 41522

American (AMR) AF: 0.151 AC: 2302 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 738 AN: 3464

East Asian (EAS) AF: 0.129 AC: 668 AN: 5170

South Asian (SAS) AF: 0.157 AC: 760 AN: 4828

European-Finnish (FIN) AF: 0.150 AC: 1584 AN: 10582

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11521 AN: 68002

Other (OTH) AF: 0.172 AC: 364 AN: 2114

Alfa AF: 0.170 Hom.: 2863

Bravo AF: 0.171

Asia WGS AF: 0.152 AC: 528 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	3.0
DANN	Benign	0.85
PhyloP100		0.041

Splicing

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

Other links and lift over

dbSNP: rs6883317; hg19: chr5-156398253;