rs10508717

Variant names:

• chr10-26383399-G-A
• rs10508717
• ENST00000646813.1:n.630-2921C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-26383399-G-A
• chr10-26383399-G-T

Variant summary

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

The ENST00000646813.1(ENSG00000284951):​n.630-2921C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 151,858 control chromosomes in the GnomAD database, including 11,721 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 0.38 (11721 hom., cov: 33)
• Consequence: ENSG00000284951 ENST00000646813.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 0 publications found

Genes affected

ENSG00000284951 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000284951	ENST00000646813.1	n.630-2921C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57612 AN: 151750 Hom.: 11726 Cov.: 33

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.379 AC: 57607 AN: 151858 Hom.: 11721 Cov.: 33 AF XY: 0.374 AC XY: 27791 AN XY: 74230

African (AFR) AF: 0.249 AC: 10325 AN: 41408

American (AMR) AF: 0.411 AC: 6279 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.600 AC: 2081 AN: 3468

East Asian (EAS) AF: 0.209 AC: 1084 AN: 5182

South Asian (SAS) AF: 0.382 AC: 1840 AN: 4820

European-Finnish (FIN) AF: 0.384 AC: 4008 AN: 10450

Middle Eastern (MID) AF: 0.528 AC: 153 AN: 290

European-Non Finnish (NFE) AF: 0.451 AC: 30638 AN: 67944

Other (OTH) AF: 0.411 AC: 868 AN: 2112

Alfa AF: 0.405 Hom.: 8459

Bravo AF: 0.376

Asia WGS AF: 0.292 AC: 1015 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.59
DANN	Benign	0.93
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs10508717; hg19: chr10-26672328;