rs34180180

Variant names:

• chr10-129466848-G-A
• rs34180180
• ENST00000735692.1:n.95+718C>T

Variant summary

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

The ENST00000735692.1(ENSG00000296036):​n.95+718C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0475 in 151,894 control chromosomes in the GnomAD database, including 273 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 0.047 (273 hom., cov: 33)
• Consequence: ENSG00000296036 ENST00000735692.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.286
• Publications: 9 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=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0625 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+718C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0475 AC: 7209 AN: 151778 Hom.: 273 Cov.: 33

Gnomad AFR AF: 0.0101

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0345

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.000390

Gnomad SAS AF: 0.0317

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.0637

Gnomad NFE AF: 0.0641

Gnomad OTH AF: 0.0489

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

GnomAD4 genome AF: 0.0475 AC: 7208 AN: 151894 Hom.: 273 Cov.: 33 AF XY: 0.0496 AC XY: 3679 AN XY: 74236

African (AFR) AF: 0.0101 AC: 417 AN: 41412

American (AMR) AF: 0.0344 AC: 526 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 367 AN: 3466

East Asian (EAS) AF: 0.000391 AC: 2 AN: 5114

South Asian (SAS) AF: 0.0316 AC: 152 AN: 4816

European-Finnish (FIN) AF: 0.119 AC: 1254 AN: 10566

Middle Eastern (MID) AF: 0.0685 AC: 20 AN: 292

European-Non Finnish (NFE) AF: 0.0641 AC: 4357 AN: 67930

Other (OTH) AF: 0.0488 AC: 103 AN: 2110

Alfa AF: 0.0517 Hom.: 382

Bravo AF: 0.0396

Asia WGS AF: 0.0120 AC: 42 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	9.3
DANN	Benign	0.86
PhyloP100		0.29
PromoterAI		-0.0040	Neutral

Splicing

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

Other links and lift over

dbSNP: rs34180180; hg19: chr10-131265112;