5-124537992-T-C

Variant names:

• chr5-124537992-T-C
• rs1494672

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 0.398 in 152,040 control chromosomes in the GnomAD database, including 12,161 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 0.40 (12161 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.694
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60407 AN: 151920 Hom.: 12152 Cov.: 32

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.398 AC: 60454 AN: 152040 Hom.: 12161 Cov.: 32 AF XY: 0.390 AC XY: 28995 AN XY: 74328

African (AFR) AF: 0.436 AC: 18084 AN: 41460

American (AMR) AF: 0.294 AC: 4497 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1363 AN: 3472

East Asian (EAS) AF: 0.278 AC: 1441 AN: 5182

South Asian (SAS) AF: 0.292 AC: 1403 AN: 4812

European-Finnish (FIN) AF: 0.374 AC: 3947 AN: 10562

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.417 AC: 28360 AN: 67970

Other (OTH) AF: 0.387 AC: 815 AN: 2108

Alfa AF: 0.401 Hom.: 19353

Bravo AF: 0.395

Asia WGS AF: 0.285 AC: 990 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.79
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs1494672; hg19: chr5-123873685;