ENST00000735692.1:n.95+899T>G

Variant names:

• chr10-129466667-A-C
• rs1625649
• ENST00000735692.1:n.95+899T>G

Variant summary

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

The ENST00000735692.1(ENSG00000296036):​n.95+899T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.61 in 151,858 control chromosomes in the GnomAD database, including 28,746 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 0.61 (28746 hom., cov: 32)
• Consequence: ENSG00000296036 ENST00000735692.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.03
• Publications: 21 publications found

Genes affected

ENSG00000296036 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.657 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
ENSG00000296036	ENST00000735692.1	n.95+899T>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92634 AN: 151740 Hom.: 28744 Cov.: 32

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.610 AC: 92656 AN: 151858 Hom.: 28746 Cov.: 32 AF XY: 0.610 AC XY: 45260 AN XY: 74178

African (AFR) AF: 0.492 AC: 20383 AN: 41426

American (AMR) AF: 0.637 AC: 9749 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.682 AC: 2364 AN: 3466

East Asian (EAS) AF: 0.676 AC: 3429 AN: 5072

South Asian (SAS) AF: 0.649 AC: 3131 AN: 4822

European-Finnish (FIN) AF: 0.630 AC: 6632 AN: 10522

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.660 AC: 44811 AN: 67934

Other (OTH) AF: 0.643 AC: 1356 AN: 2110

Alfa AF: 0.629 Hom.: 3793

Bravo AF: 0.607

Asia WGS AF: 0.647 AC: 2251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.7
DANN	Benign	0.40
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs1625649; hg19: chr10-131264931;