rs2588350

Variant names:

• chr12-10800458-T-C
• rs2588350

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 0.746 in 152,056 control chromosomes in the GnomAD database, including 42,517 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 0.75 (42517 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720
• Publications: 8 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 (NFE) allele frequency at 95% confidence interval = 0.769 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: 0.746 AC: 113313 AN: 151938 Hom.: 42482 Cov.: 32

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.923

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.831

Gnomad EAS AF: 0.723

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.755

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

GnomAD4 genome AF: 0.746 AC: 113393 AN: 152056 Hom.: 42517 Cov.: 32 AF XY: 0.745 AC XY: 55384 AN XY: 74326

African (AFR) AF: 0.684 AC: 28364 AN: 41486

American (AMR) AF: 0.728 AC: 11105 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.831 AC: 2883 AN: 3468

East Asian (EAS) AF: 0.723 AC: 3727 AN: 5156

South Asian (SAS) AF: 0.686 AC: 3311 AN: 4830

European-Finnish (FIN) AF: 0.822 AC: 8714 AN: 10596

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.774 AC: 52616 AN: 67944

Other (OTH) AF: 0.754 AC: 1591 AN: 2110

Alfa AF: 0.765 Hom.: 169161

Bravo AF: 0.735

Asia WGS AF: 0.705 AC: 2451 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	1.7
DANN	Benign	0.74
PhyloP100		-0.072

Splicing

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

Other links and lift over

dbSNP: rs2588350; hg19: chr12-10953057;