rs4972593

Variant names:

• chr2-173598126-T-A
• rs4972593

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 0.2 in 152,022 control chromosomes in the GnomAD database, including 3,554 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 0.20 (3554 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.166

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.341 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: 0.200 AC: 30400 AN: 151904 Hom.: 3551 Cov.: 32

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.200 AC: 30423 AN: 152022 Hom.: 3554 Cov.: 32 AF XY: 0.198 AC XY: 14687 AN XY: 74322

Gnomad4 AFR AF: 0.306

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.228

Gnomad4 EAS AF: 0.200

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.199

Alfa AF: 0.180 Hom.: 318

Bravo AF: 0.201

Asia WGS AF: 0.287 AC: 997 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4972593; hg19: chr2-174462854;