10-3331986-C-T

Variant names:

• chr10-3331986-C-T
• rs735155
• ENST00000783251.1:n.80C>T

Variant summary

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

The ENST00000783251.1(ENSG00000286610):​n.80C>T 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 0.44 in 151,870 control chromosomes in the GnomAD database, including 15,599 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 0.44 (15599 hom., cov: 31)
• Consequence: ENSG00000286610 ENST00000783251.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.59
• Publications: 14 publications found

Genes affected

ENSG00000286610 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376360	NR_131187.1	n.162+13130C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286610	ENST00000783251.1	n.80C>T		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000286610	ENST00000783245.1	n.1044+13130C>T		intron_variant	Intron 1 of 1
ENSG00000286610	ENST00000783246.1	n.351+13130C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.441 AC: 66869 AN: 151752 Hom.: 15597 Cov.: 31

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.440 AC: 66881 AN: 151870 Hom.: 15599 Cov.: 31 AF XY: 0.450 AC XY: 33416 AN XY: 74204

African (AFR) AF: 0.322 AC: 13320 AN: 41412

American (AMR) AF: 0.490 AC: 7488 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1895 AN: 3472

East Asian (EAS) AF: 0.819 AC: 4182 AN: 5106

South Asian (SAS) AF: 0.628 AC: 3026 AN: 4820

European-Finnish (FIN) AF: 0.491 AC: 5193 AN: 10566

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.446 AC: 30304 AN: 67920

Other (OTH) AF: 0.484 AC: 1016 AN: 2100

Alfa AF: 0.444 Hom.: 23751

Bravo AF: 0.433

Asia WGS AF: 0.662 AC: 2305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.073
DANN	Benign	0.80
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs735155; hg19: chr10-3374178;