chr5-2724248-T-C

Variant names:

• chr5-2724248-T-C
• rs2173226

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 0.393 in 151,834 control chromosomes in the GnomAD database, including 12,522 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 0.39 (12522 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.11).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.54 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: 0.393 AC: 59641 AN: 151714 Hom.: 12497 Cov.: 32

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.393 AC: 59721 AN: 151834 Hom.: 12522 Cov.: 32 AF XY: 0.391 AC XY: 29033 AN XY: 74194

African (AFR) AF: 0.546 AC: 22561 AN: 41346

American (AMR) AF: 0.369 AC: 5634 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1302 AN: 3466

East Asian (EAS) AF: 0.319 AC: 1636 AN: 5128

South Asian (SAS) AF: 0.384 AC: 1849 AN: 4810

European-Finnish (FIN) AF: 0.339 AC: 3567 AN: 10532

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.323 AC: 21976 AN: 67960

Other (OTH) AF: 0.374 AC: 791 AN: 2116

Alfa AF: 0.354 Hom.: 26443

Bravo AF: 0.400

Asia WGS AF: 0.410 AC: 1428 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.050
DANN	Benign	0.12
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2173226; hg19: chr5-2724362;