chr5-124538305-C-T

Variant names:

• chr5-124538305-C-T
• rs1494673

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 0.124 in 152,170 control chromosomes in the GnomAD database, including 1,397 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 0.12 (1397 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.704
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.17 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: 0.124 AC: 18866 AN: 152052 Hom.: 1398 Cov.: 32

Gnomad AFR AF: 0.0399

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.124 AC: 18858 AN: 152170 Hom.: 1397 Cov.: 32 AF XY: 0.123 AC XY: 9164 AN XY: 74392

African (AFR) AF: 0.0398 AC: 1654 AN: 41514

American (AMR) AF: 0.112 AC: 1710 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 376 AN: 3472

East Asian (EAS) AF: 0.101 AC: 525 AN: 5180

South Asian (SAS) AF: 0.122 AC: 588 AN: 4818

European-Finnish (FIN) AF: 0.164 AC: 1730 AN: 10574

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11764 AN: 68014

Other (OTH) AF: 0.129 AC: 273 AN: 2110

Alfa AF: 0.155 Hom.: 6016

Bravo AF: 0.116

Asia WGS AF: 0.106 AC: 367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.81
DANN	Benign	0.26
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs1494673; hg19: chr5-123873998;