rs2173226

Positions:

• chr5-2724248-T-C
• chr5-2724248-T-G

Variant summary

Our verdict is Benign. Variant got -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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.2724248T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.546

Gnomad4 AMR AF: 0.369

Gnomad4 ASJ AF: 0.376

Gnomad4 EAS AF: 0.319

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.339

Gnomad4 NFE AF: 0.323

Gnomad4 OTH AF: 0.374

Alfa AF: 0.339 Hom.: 8380

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2173226; hg19: chr5-2724362;