rs2393886

Variant names:

• chr10-62498584-C-T
• rs2393886
• ENST00000647733.1:c.981+38787C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000647733.1(ENSG00000285837):​c.981+38787C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 152,004 control chromosomes in the GnomAD database, including 26,052 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 0.57 (26052 hom., cov: 32)
• Consequence: ENSG00000285837 ENST00000647733.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.230
• Publications: 2 publications found

Genes affected

ENSG00000285837 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.767 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
ENSG00000285837	ENST00000647733.1	c.981+38787C>T		intron_variant	Intron 4 of 7			ENSP00000502188.1

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86596 AN: 151884 Hom.: 25999 Cov.: 32

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.458

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.570 AC: 86708 AN: 152004 Hom.: 26052 Cov.: 32 AF XY: 0.568 AC XY: 42199 AN XY: 74298

African (AFR) AF: 0.774 AC: 32092 AN: 41470

American (AMR) AF: 0.510 AC: 7789 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 1736 AN: 3468

East Asian (EAS) AF: 0.521 AC: 2686 AN: 5160

South Asian (SAS) AF: 0.512 AC: 2467 AN: 4822

European-Finnish (FIN) AF: 0.526 AC: 5547 AN: 10550

Middle Eastern (MID) AF: 0.459 AC: 133 AN: 290

European-Non Finnish (NFE) AF: 0.479 AC: 32569 AN: 67960

Other (OTH) AF: 0.536 AC: 1131 AN: 2110

Alfa AF: 0.506 Hom.: 9456

Bravo AF: 0.578

Asia WGS AF: 0.541 AC: 1879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	0.73
DANN	Benign	0.49
PhyloP100		-0.23
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2393886; hg19: chr10-64258343;