rs2453737

Variant names:

• chr5-175431899-T-C
• rs2453737

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 0.43 in 151,878 control chromosomes in the GnomAD database, including 14,380 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 0.43 (14380 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.282
• Publications: 5 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 = 0.534 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: 0.430 AC: 65199 AN: 151758 Hom.: 14356 Cov.: 32

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.430 AC: 65277 AN: 151878 Hom.: 14380 Cov.: 32 AF XY: 0.428 AC XY: 31734 AN XY: 74206

African (AFR) AF: 0.540 AC: 22370 AN: 41408

American (AMR) AF: 0.433 AC: 6594 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1563 AN: 3468

East Asian (EAS) AF: 0.387 AC: 1988 AN: 5136

South Asian (SAS) AF: 0.401 AC: 1932 AN: 4816

European-Finnish (FIN) AF: 0.340 AC: 3589 AN: 10556

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.382 AC: 25953 AN: 67940

Other (OTH) AF: 0.432 AC: 909 AN: 2106

Alfa AF: 0.403 Hom.: 36551

Bravo AF: 0.439

Asia WGS AF: 0.418 AC: 1455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.5
DANN	Benign	0.44
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs2453737; hg19: chr5-174858902; COSMIC: COSV60236646;