10-129465567-G-A

Variant names:

• chr10-129465567-G-A
• rs10764881
• ENST00000735692.1:n.96-1784C>T

Variant summary

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

The ENST00000735692.1(ENSG00000296036):​n.96-1784C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 152,142 control chromosomes in the GnomAD database, including 5,664 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 0.25 (5664 hom., cov: 32)
• Consequence: ENSG00000296036 ENST00000735692.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.181
• 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.313 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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296036	ENST00000735692.1		n.96-1784C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38291 AN: 152024 Hom.: 5649 Cov.: 32

Gnomad AFR AF: 0.0937

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.252 AC: 38318 AN: 152142 Hom.: 5664 Cov.: 32 AF XY: 0.253 AC XY: 18809 AN XY: 74366

African (AFR) AF: 0.0935 AC: 3883 AN: 41526

American (AMR) AF: 0.309 AC: 4720 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1073 AN: 3466

East Asian (EAS) AF: 0.323 AC: 1672 AN: 5172

South Asian (SAS) AF: 0.300 AC: 1444 AN: 4814

European-Finnish (FIN) AF: 0.290 AC: 3070 AN: 10586

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.317 AC: 21553 AN: 67982

Other (OTH) AF: 0.245 AC: 517 AN: 2114

Alfa AF: 0.300 Hom.: 1954

Bravo AF: 0.246

Asia WGS AF: 0.291 AC: 1011 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.4
DANN	Benign	0.83
PhyloP100		0.18

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10764881;

hg19: chr10-131263831;