2-237913557-G-C

Variant names:

• chr2-237913557-G-C
• rs7590387

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 0.552 in 152,068 control chromosomes in the GnomAD database, including 24,719 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 0.55 (24719 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.473
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.75 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83836 AN: 151950 Hom.: 24677 Cov.: 33

Gnomad AFR AF: 0.756

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.552 AC: 83929 AN: 152068 Hom.: 24719 Cov.: 33 AF XY: 0.546 AC XY: 40548 AN XY: 74330

African (AFR) AF: 0.757 AC: 31399 AN: 41498

American (AMR) AF: 0.425 AC: 6492 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.609 AC: 2115 AN: 3472

East Asian (EAS) AF: 0.269 AC: 1377 AN: 5128

South Asian (SAS) AF: 0.499 AC: 2404 AN: 4822

European-Finnish (FIN) AF: 0.483 AC: 5108 AN: 10568

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.488 AC: 33164 AN: 67990

Other (OTH) AF: 0.553 AC: 1168 AN: 2114

Alfa AF: 0.349 Hom.: 823

Bravo AF: 0.554

Asia WGS AF: 0.416 AC: 1448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.29
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs7590387; hg19: chr2-238822199;