16-64793581-T-G

Variant names:

• chr16-64793581-T-G
• rs1424003

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

The variant allele was found at a frequency of 0.0932 in 152,060 control chromosomes in the GnomAD database, including 864 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 0.093 (864 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.96
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.15).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.138 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: 0.0932 AC: 14166 AN: 151942 Hom.: 863 Cov.: 32

Gnomad AFR AF: 0.0236

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.0809

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.000775

Gnomad SAS AF: 0.0799

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.0932 AC: 14168 AN: 152060 Hom.: 864 Cov.: 32 AF XY: 0.0911 AC XY: 6772 AN XY: 74340

African (AFR) AF: 0.0235 AC: 976 AN: 41532

American (AMR) AF: 0.0807 AC: 1230 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 512 AN: 3466

East Asian (EAS) AF: 0.000972 AC: 5 AN: 5146

South Asian (SAS) AF: 0.0806 AC: 389 AN: 4826

European-Finnish (FIN) AF: 0.105 AC: 1117 AN: 10594

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9520 AN: 67940

Other (OTH) AF: 0.106 AC: 223 AN: 2110

Alfa AF: 0.0980 Hom.: 252

Bravo AF: 0.0906

Asia WGS AF: 0.0340 AC: 118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.15
CADD	Benign	23
DANN	Benign	0.77
PhyloP100		5.0

Splicing

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

Other links and lift over

dbSNP: rs1424003; hg19: chr16-64827484;