chr5-123271329-C-T

Variant names:

• chr5-123271329-C-T
• rs255628

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 0.717 in 152,170 control chromosomes in the GnomAD database, including 39,371 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 0.72 (39371 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.518
• Publications: 8 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 (EAS) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.717 AC: 109022 AN: 152052 Hom.: 39331 Cov.: 32

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.606

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.863

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.692

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

GnomAD4 genome AF: 0.717 AC: 109116 AN: 152170 Hom.: 39371 Cov.: 32 AF XY: 0.720 AC XY: 53539 AN XY: 74384

African (AFR) AF: 0.774 AC: 32166 AN: 41532

American (AMR) AF: 0.678 AC: 10371 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.612 AC: 2126 AN: 3472

East Asian (EAS) AF: 0.863 AC: 4467 AN: 5176

South Asian (SAS) AF: 0.752 AC: 3626 AN: 4824

European-Finnish (FIN) AF: 0.720 AC: 7617 AN: 10578

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.685 AC: 46545 AN: 67984

Other (OTH) AF: 0.690 AC: 1456 AN: 2110

Alfa AF: 0.692 Hom.: 159807

Bravo AF: 0.714

Asia WGS AF: 0.778 AC: 2708 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	4.9
DANN	Benign	0.52
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs255628; hg19: chr5-122607023; COSMIC: COSV60191845;