rs10510144

Variant names:

• chr10-125491278-G-A
• rs10510144
• ENST00000813024.1:n.323+2562C>T

Variant summary

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

The ENST00000813024.1(ENSG00000305803):​n.323+2562C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 152,006 control chromosomes in the GnomAD database, including 4,685 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 0.22 (4685 hom., cov: 32)
• Consequence: ENSG00000305803 ENST00000813024.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.902
• Publications: 2 publications found

Genes affected

ENSG00000305803 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378543	XR_007062331.1	n.315+2562C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305803	ENST00000813024.1	n.323+2562C>T		intron_variant	Intron 1 of 2
ENSG00000305803	ENST00000813025.1	n.315+2562C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.224 AC: 34036 AN: 151888 Hom.: 4692 Cov.: 32

Gnomad AFR AF: 0.0708

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.224 AC: 34026 AN: 152006 Hom.: 4685 Cov.: 32 AF XY: 0.232 AC XY: 17256 AN XY: 74280

African (AFR) AF: 0.0708 AC: 2936 AN: 41494

American (AMR) AF: 0.245 AC: 3748 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1114 AN: 3460

East Asian (EAS) AF: 0.421 AC: 2171 AN: 5156

South Asian (SAS) AF: 0.324 AC: 1562 AN: 4814

European-Finnish (FIN) AF: 0.345 AC: 3637 AN: 10528

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.266 AC: 18065 AN: 67972

Other (OTH) AF: 0.236 AC: 498 AN: 2106

Alfa AF: 0.259 Hom.: 4122

Bravo AF: 0.208

Asia WGS AF: 0.313 AC: 1089 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.80
DANN	Benign	0.62
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs10510144; hg19: chr10-127179847;