5-170145727-C-T

Variant names:

• chr5-170145727-C-T
• rs2879278

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 0.328 in 151,972 control chromosomes in the GnomAD database, including 8,877 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 0.33 (8877 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.57
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.407 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: 0.328 AC: 49822 AN: 151854 Hom.: 8881 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.328 AC: 49807 AN: 151972 Hom.: 8877 Cov.: 32 AF XY: 0.326 AC XY: 24218 AN XY: 74276

African (AFR) AF: 0.177 AC: 7341 AN: 41472

American (AMR) AF: 0.358 AC: 5475 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1270 AN: 3470

East Asian (EAS) AF: 0.330 AC: 1698 AN: 5150

South Asian (SAS) AF: 0.330 AC: 1587 AN: 4802

European-Finnish (FIN) AF: 0.320 AC: 3377 AN: 10552

Middle Eastern (MID) AF: 0.247 AC: 72 AN: 292

European-Non Finnish (NFE) AF: 0.411 AC: 27921 AN: 67940

Other (OTH) AF: 0.302 AC: 638 AN: 2114

Alfa AF: 0.386 Hom.: 10707

Bravo AF: 0.323

Asia WGS AF: 0.314 AC: 1088 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.64
DANN	Benign	0.95
PhyloP100		-4.6

Splicing

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

Other links and lift over

dbSNP: rs2879278; hg19: chr5-169572731;