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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000738127.1. 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
	ENSG00000287023	ENST00000738127.1		n.761+25468T>C		intron	N/A
	ENSG00000287023	ENST00000738128.1		n.687+25468T>C		intron	N/A
	ENSG00000287023	ENST00000738129.1		n.230+25468T>C		intron	N/A

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 v4.9

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

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

Other links and lift over

dbSNP: rs10508288;

hg19: chr10-4781029;