10-129466317-T-G

Variant names:

• chr10-129466317-T-G
• rs1711646
• ENST00000735692.1:n.95+1249A>C

Variant summary

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

The ENST00000735692.1(ENSG00000296036):​n.95+1249A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.702 in 151,938 control chromosomes in the GnomAD database, including 40,750 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 0.70 (40750 hom., cov: 31)
• Consequence: ENSG00000296036 ENST00000735692.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.792
• Publications: 7 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.958 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000735692.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296036	ENST00000735692.1		n.95+1249A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.702 AC: 106642 AN: 151820 Hom.: 40742 Cov.: 31

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.853

Gnomad AMR AF: 0.798

Gnomad ASJ AF: 0.821

Gnomad EAS AF: 0.980

Gnomad SAS AF: 0.867

Gnomad FIN AF: 0.763

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.829

Gnomad OTH AF: 0.736

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

GnomAD4 genome AF: 0.702 AC: 106671 AN: 151938 Hom.: 40750 Cov.: 31 AF XY: 0.705 AC XY: 52357 AN XY: 74220

African (AFR) AF: 0.374 AC: 15493 AN: 41426

American (AMR) AF: 0.798 AC: 12197 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.821 AC: 2850 AN: 3470

East Asian (EAS) AF: 0.981 AC: 5009 AN: 5108

South Asian (SAS) AF: 0.867 AC: 4164 AN: 4804

European-Finnish (FIN) AF: 0.763 AC: 8053 AN: 10550

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.829 AC: 56347 AN: 67976

Other (OTH) AF: 0.737 AC: 1558 AN: 2114

Alfa AF: 0.770 Hom.: 20102

Bravo AF: 0.690

Asia WGS AF: 0.876 AC: 3046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.5
DANN	Benign	0.42
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs1711646; hg19: chr10-131264581;