chr10-2523893-C-T

Variant names:

• chr10-2523893-C-T
• rs2388097
• ENST00000437289.1:n.188-13600C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000437289.1(ENSG00000235281):​n.188-13600C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 152,042 control chromosomes in the GnomAD database, including 22,998 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 0.53 (22998 hom., cov: 32)
• Consequence: ENSG00000235281 ENST00000437289.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.174

Genes affected

ENSG00000235281 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376350	NR_188171.1	n.137+21904C>T		intron_variant	Intron 1 of 5
LOC105376350	NR_188172.1	n.137+21904C>T		intron_variant	Intron 1 of 4
LOC105376350	NR_188173.1	n.137+21904C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000235281	ENST00000437289.1	n.188-13600C>T		intron_variant	Intron 1 of 1	3
ENSG00000235281	ENST00000438753.1	n.207+21904C>T		intron_variant	Intron 1 of 1	5
ENSG00000235281	ENST00000656735.1	n.364+21904C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.527 AC: 80013 AN: 151924 Hom.: 22995 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.656

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.526 AC: 80029 AN: 152042 Hom.: 22998 Cov.: 32 AF XY: 0.525 AC XY: 39020 AN XY: 74340

Gnomad4 AFR AF: 0.293

Gnomad4 AMR AF: 0.537

Gnomad4 ASJ AF: 0.533

Gnomad4 EAS AF: 0.417

Gnomad4 SAS AF: 0.503

Gnomad4 FIN AF: 0.638

Gnomad4 NFE AF: 0.656

Gnomad4 OTH AF: 0.558

Alfa AF: 0.626 Hom.: 37006

Bravo AF: 0.511

Asia WGS AF: 0.434 AC: 1510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.74
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2388097; hg19: chr10-2566085;