5-79372110-A-T

Variant names:

• chr5-79372110-A-T
• rs2290639

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 0.538 in 151,772 control chromosomes in the GnomAD database, including 25,647 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 0.54 (25647 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.97
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.868 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: 0.537 AC: 81460 AN: 151654 Hom.: 25580 Cov.: 30

Gnomad AFR AF: 0.875

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.657

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.538 AC: 81588 AN: 151772 Hom.: 25647 Cov.: 30 AF XY: 0.540 AC XY: 40018 AN XY: 74166

African (AFR) AF: 0.876 AC: 36274 AN: 41426

American (AMR) AF: 0.527 AC: 8065 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1843 AN: 3464

East Asian (EAS) AF: 0.658 AC: 3392 AN: 5156

South Asian (SAS) AF: 0.467 AC: 2241 AN: 4796

European-Finnish (FIN) AF: 0.365 AC: 3819 AN: 10458

Middle Eastern (MID) AF: 0.432 AC: 126 AN: 292

European-Non Finnish (NFE) AF: 0.359 AC: 24393 AN: 67872

Other (OTH) AF: 0.528 AC: 1114 AN: 2108

Alfa AF: 0.464 Hom.: 2353

Bravo AF: 0.565

Asia WGS AF: 0.625 AC: 2174 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.083
DANN	Benign	0.43
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs2290639; hg19: chr5-78667933;