chr10-4763511-G-A

Variant names:

• chr10-4763511-G-A
• rs10508290
• ENST00000670284.1:n.529+794C>T

Variant summary

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

The ENST00000670284.1(ENSG00000287023):​n.529+794C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.096 in 152,110 control chromosomes in the GnomAD database, including 1,730 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 0.096 (1730 hom., cov: 32)
• Consequence: ENSG00000287023 ENST00000670284.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.675
• Publications: 3 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376374	XR_930598.3	n.79+455C>T		intron_variant	Intron 1 of 2
LOC105376375	XR_930599.2	n.534+794C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287023	ENST00000670284.1	n.529+794C>T		intron_variant	Intron 2 of 3
ENSG00000287023	ENST00000701197.2	n.700+794C>T		intron_variant	Intron 2 of 2
ENSG00000287023	ENST00000738127.1	n.761+794C>T		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.0960 AC: 14595 AN: 151992 Hom.: 1729 Cov.: 32

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0413

Gnomad ASJ AF: 0.0430

Gnomad EAS AF: 0.511

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.0378

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0195

Gnomad OTH AF: 0.0760

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

GnomAD4 genome AF: 0.0960 AC: 14610 AN: 152110 Hom.: 1730 Cov.: 32 AF XY: 0.0995 AC XY: 7402 AN XY: 74378

African (AFR) AF: 0.201 AC: 8328 AN: 41472

American (AMR) AF: 0.0412 AC: 630 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0430 AC: 149 AN: 3462

East Asian (EAS) AF: 0.511 AC: 2635 AN: 5158

South Asian (SAS) AF: 0.193 AC: 929 AN: 4818

European-Finnish (FIN) AF: 0.0378 AC: 400 AN: 10582

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0195 AC: 1325 AN: 68020

Other (OTH) AF: 0.0799 AC: 169 AN: 2114

Alfa AF: 0.0516 Hom.: 2201

Bravo AF: 0.0986

Asia WGS AF: 0.334 AC: 1157 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.78
DANN	Benign	0.67
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs10508290; hg19: chr10-4805703;