10-15929236-A-G

Variant names:

• chr10-15929236-A-G
• rs1010242
• ENST00000719107.1:n.461+27172A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000719107.1(ENSG00000293799):​n.461+27172A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 152,034 control chromosomes in the GnomAD database, including 13,553 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 (13553 hom., cov: 32)
• Consequence: ENSG00000293799 ENST00000719107.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.56
• Publications: 6 publications found

Genes affected

ENSG00000293799 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.892 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
ENSG00000293799	ENST00000719107.1	n.461+27172A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58221 AN: 151918 Hom.: 13546 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.913

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.383 AC: 58246 AN: 152034 Hom.: 13553 Cov.: 32 AF XY: 0.398 AC XY: 29603 AN XY: 74334

African (AFR) AF: 0.141 AC: 5845 AN: 41500

American (AMR) AF: 0.519 AC: 7921 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1280 AN: 3464

East Asian (EAS) AF: 0.913 AC: 4733 AN: 5182

South Asian (SAS) AF: 0.608 AC: 2927 AN: 4814

European-Finnish (FIN) AF: 0.503 AC: 5305 AN: 10554

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.425 AC: 28885 AN: 67934

Other (OTH) AF: 0.409 AC: 864 AN: 2110

Alfa AF: 0.411 Hom.: 30490

Bravo AF: 0.369

Asia WGS AF: 0.723 AC: 2509 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	19
DANN	Benign	0.70
PhyloP100		2.6

Splicing

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

Other links and lift over

dbSNP: rs1010242; hg19: chr10-15971235;