10-129035457-A-G

Variant names:

• chr10-129035457-A-G
• rs4750727
• ENST00000685374.3:n.1141T>C

Variant summary

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

The ENST00000685374.3(ENSG00000289400):​n.1141T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0787 in 152,306 control chromosomes in the GnomAD database, including 1,027 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 0.079 (1027 hom., cov: 33)
• Consequence: ENSG00000289400 ENST00000685374.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.471
• Publications: 1 publications found

Genes affected

ENSG00000289400 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000685374.3. 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
	ENSG00000289400	ENST00000685374.3		n.1141T>C		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000289400	ENST00000688275.2		n.813T>C		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000289400	ENST00000689194.2		n.1182T>C		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0785 AC: 11947 AN: 152188 Hom.: 1017 Cov.: 33

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0478

Gnomad ASJ AF: 0.0101

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.0172

Gnomad FIN AF: 0.0148

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0202

Gnomad OTH AF: 0.0626

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

GnomAD4 genome AF: 0.0787 AC: 11992 AN: 152306 Hom.: 1027 Cov.: 33 AF XY: 0.0774 AC XY: 5762 AN XY: 74488

African (AFR) AF: 0.215 AC: 8918 AN: 41540

American (AMR) AF: 0.0478 AC: 731 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0101 AC: 35 AN: 3472

East Asian (EAS) AF: 0.108 AC: 558 AN: 5184

South Asian (SAS) AF: 0.0172 AC: 83 AN: 4824

European-Finnish (FIN) AF: 0.0148 AC: 157 AN: 10630

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0202 AC: 1373 AN: 68036

Other (OTH) AF: 0.0619 AC: 131 AN: 2116

Alfa AF: 0.0522 Hom.: 798

Bravo AF: 0.0879

Asia WGS AF: 0.0700 AC: 244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.37
DANN	Benign	0.62
PhyloP100		-0.47

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: rs4750727;

hg19: chr10-130833721;