chr5-164084985-A-G

Variant names:

• chr5-164084985-A-G
• rs9313999

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 0.617 in 151,724 control chromosomes in the GnomAD database, including 29,297 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 0.62 (29297 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.204
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.732 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: 0.616 AC: 93450 AN: 151606 Hom.: 29264 Cov.: 31

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.614

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

GnomAD4 genome AF: 0.617 AC: 93538 AN: 151724 Hom.: 29297 Cov.: 31 AF XY: 0.613 AC XY: 45384 AN XY: 74090

African (AFR) AF: 0.739 AC: 30596 AN: 41388

American (AMR) AF: 0.594 AC: 9027 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 1793 AN: 3468

East Asian (EAS) AF: 0.555 AC: 2854 AN: 5138

South Asian (SAS) AF: 0.469 AC: 2261 AN: 4818

European-Finnish (FIN) AF: 0.541 AC: 5660 AN: 10468

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.582 AC: 39543 AN: 67932

Other (OTH) AF: 0.610 AC: 1288 AN: 2110

Alfa AF: 0.592 Hom.: 79942

Bravo AF: 0.623

Asia WGS AF: 0.505 AC: 1750 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.3
DANN	Benign	0.42
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs9313999; hg19: chr5-163511991;