rs10508288

Variant names:

• chr10-4738837-A-G
• rs10508288
• ENST00000738127.1:n.761+25468T>C

Variant summary

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

The ENST00000738127.1(ENSG00000287023):​n.761+25468T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 151,352 control chromosomes in the GnomAD database, including 9,036 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 0.32 (9036 hom., cov: 28)
• Consequence: ENSG00000287023 ENST00000738127.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310
• Publications: 2 publications found

Genes affected

ENSG00000287023 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) 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
LOC105376375	XR_930599.2	n.534+25468T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287023	ENST00000738127.1	n.761+25468T>C		intron_variant	Intron 2 of 5
ENSG00000287023	ENST00000738128.1	n.687+25468T>C		intron_variant	Intron 2 of 4
ENSG00000287023	ENST00000738129.1	n.230+25468T>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.324 AC: 48939 AN: 151248 Hom.: 9028 Cov.: 28

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.349

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.324 AC: 48969 AN: 151352 Hom.: 9036 Cov.: 28 AF XY: 0.325 AC XY: 23989 AN XY: 73902

African (AFR) AF: 0.140 AC: 5774 AN: 41282

American (AMR) AF: 0.401 AC: 6083 AN: 15152

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1223 AN: 3464

East Asian (EAS) AF: 0.227 AC: 1167 AN: 5152

South Asian (SAS) AF: 0.349 AC: 1672 AN: 4796

European-Finnish (FIN) AF: 0.405 AC: 4194 AN: 10366

Middle Eastern (MID) AF: 0.347 AC: 100 AN: 288

European-Non Finnish (NFE) AF: 0.410 AC: 27810 AN: 67838

Other (OTH) AF: 0.346 AC: 728 AN: 2102

Alfa AF: 0.388 Hom.: 26024

Bravo AF: 0.314

Asia WGS AF: 0.298 AC: 1040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.8
DANN	Benign	0.48
PhyloP100		-0.031

Splicing

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

Other links and lift over

dbSNP: rs10508288; hg19: chr10-4781029;