rs16901064

Variant names:

• chr5-31386890-C-A
• rs16901064

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 0.167 in 152,118 control chromosomes in the GnomAD database, including 2,160 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 (2160 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.253 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: 0.167 AC: 25438 AN: 151998 Hom.: 2160 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.167 AC: 25461 AN: 152118 Hom.: 2160 Cov.: 32 AF XY: 0.169 AC XY: 12598 AN XY: 74376

African (AFR) AF: 0.160 AC: 6648 AN: 41500

American (AMR) AF: 0.193 AC: 2942 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 621 AN: 3470

East Asian (EAS) AF: 0.265 AC: 1370 AN: 5176

South Asian (SAS) AF: 0.213 AC: 1024 AN: 4816

European-Finnish (FIN) AF: 0.160 AC: 1697 AN: 10578

Middle Eastern (MID) AF: 0.216 AC: 63 AN: 292

European-Non Finnish (NFE) AF: 0.157 AC: 10648 AN: 67984

Other (OTH) AF: 0.160 AC: 337 AN: 2112

Alfa AF: 0.161 Hom.: 5901

Bravo AF: 0.166

Asia WGS AF: 0.247 AC: 859 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.5
DANN	Benign	0.73
PhyloP100		-0.038

Splicing

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

Other links and lift over

dbSNP: rs16901064; hg19: chr5-31386997;