rs1597944

Positions:

• chr2-233595452-C-T

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 0.444 in 151,950 control chromosomes in the GnomAD database, including 16,577 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 0.44 (16577 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67387 AN: 151832 Hom.: 16572 Cov.: 31

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.633

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.444 AC: 67419 AN: 151950 Hom.: 16577 Cov.: 31 AF XY: 0.451 AC XY: 33514 AN XY: 74246

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.478

Gnomad4 ASJ AF: 0.548

Gnomad4 EAS AF: 0.539

Gnomad4 SAS AF: 0.661

Gnomad4 FIN AF: 0.523

Gnomad4 NFE AF: 0.529

Gnomad4 OTH AF: 0.456

Alfa AF: 0.516 Hom.: 26582

Bravo AF: 0.425

Asia WGS AF: 0.580 AC: 2013 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	2.2
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1597944; hg19: chr2-234504098;