rs2393352

Variant names:

• chr10-57512004-T-C
• rs2393352

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 0.511 in 151,988 control chromosomes in the GnomAD database, including 20,136 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 0.51 (20136 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.700
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.788 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: 0.511 AC: 77564 AN: 151870 Hom.: 20135 Cov.: 32

Gnomad AFR AF: 0.479

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.511 AC: 77598 AN: 151988 Hom.: 20136 Cov.: 32 AF XY: 0.512 AC XY: 38055 AN XY: 74272

African (AFR) AF: 0.479 AC: 19872 AN: 41472

American (AMR) AF: 0.556 AC: 8482 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1717 AN: 3468

East Asian (EAS) AF: 0.809 AC: 4174 AN: 5160

South Asian (SAS) AF: 0.366 AC: 1766 AN: 4826

European-Finnish (FIN) AF: 0.512 AC: 5407 AN: 10556

Middle Eastern (MID) AF: 0.569 AC: 165 AN: 290

European-Non Finnish (NFE) AF: 0.507 AC: 34445 AN: 67932

Other (OTH) AF: 0.498 AC: 1051 AN: 2112

Alfa AF: 0.495 Hom.: 3046

Bravo AF: 0.517

Asia WGS AF: 0.531 AC: 1843 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.5
DANN	Benign	0.88
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs2393352; hg19: chr10-59271764;