rs7590983

Positions:

• chr2-173497621-T-C

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 0.133 in 152,234 control chromosomes in the GnomAD database, including 2,154 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 0.13 (2154 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.244

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20210 AN: 152116 Hom.: 2147 Cov.: 32

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0839

Gnomad ASJ AF: 0.0536

Gnomad EAS AF: 0.0354

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0499

Gnomad MID AF: 0.0924

Gnomad NFE AF: 0.0676

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.133 AC: 20224 AN: 152234 Hom.: 2154 Cov.: 32 AF XY: 0.130 AC XY: 9690 AN XY: 74458

Gnomad4 AFR AF: 0.305

Gnomad4 AMR AF: 0.0837

Gnomad4 ASJ AF: 0.0536

Gnomad4 EAS AF: 0.0349

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.0499

Gnomad4 NFE AF: 0.0676

Gnomad4 OTH AF: 0.119

Alfa AF: 0.0750 Hom.: 917

Bravo AF: 0.142

Asia WGS AF: 0.0680 AC: 236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.7
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7590983; hg19: chr2-174362349;