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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000813024.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305803	ENST00000813024.1		n.323+2562C>T		intron	N/A
	ENSG00000305803	ENST00000813025.1		n.315+2562C>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10510144;

hg19: chr10-127179847;