rs7590305

Variant names:

• chr2-88213612-C-T
• rs7590305

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 0.433 in 152,114 control chromosomes in the GnomAD database, including 16,109 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 0.43 (16109 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.554 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: 0.433 AC: 65822 AN: 151996 Hom.: 16117 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.433 AC: 65815 AN: 152114 Hom.: 16109 Cov.: 32 AF XY: 0.432 AC XY: 32106 AN XY: 74366

African (AFR) AF: 0.222 AC: 9228 AN: 41484

American (AMR) AF: 0.418 AC: 6386 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.599 AC: 2079 AN: 3472

East Asian (EAS) AF: 0.212 AC: 1100 AN: 5178

South Asian (SAS) AF: 0.348 AC: 1678 AN: 4820

European-Finnish (FIN) AF: 0.535 AC: 5666 AN: 10594

Middle Eastern (MID) AF: 0.616 AC: 180 AN: 292

European-Non Finnish (NFE) AF: 0.558 AC: 37958 AN: 67980

Other (OTH) AF: 0.501 AC: 1060 AN: 2114

Alfa AF: 0.519 Hom.: 89256

Bravo AF: 0.411

Asia WGS AF: 0.292 AC: 1018 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.20
DANN	Benign	0.20
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs7590305; hg19: chr2-88513131;