rs7590983

Variant names:

• chr2-173497621-T-C
• rs7590983

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 0.133 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.305 AC: 12662 AN: 41510

American (AMR) AF: 0.0837 AC: 1281 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0536 AC: 186 AN: 3470

East Asian (EAS) AF: 0.0349 AC: 181 AN: 5182

South Asian (SAS) AF: 0.102 AC: 492 AN: 4824

European-Finnish (FIN) AF: 0.0499 AC: 530 AN: 10612

Middle Eastern (MID) AF: 0.0856 AC: 25 AN: 292

European-Non Finnish (NFE) AF: 0.0676 AC: 4599 AN: 68016

Other (OTH) AF: 0.119 AC: 251 AN: 2114

Alfa AF: 0.0851 Hom.: 2970

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
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs7590983; hg19: chr2-174362349;