chr10-3366755-A-C

Variant names:

• chr10-3366755-A-C
• rs17135159
• ENST00000783245.1:n.1045-32350A>C

Variant summary

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

The ENST00000783245.1(ENSG00000286610):​n.1045-32350A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 152,100 control chromosomes in the GnomAD database, including 3,586 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 0.21 (3586 hom., cov: 32)
• Consequence: ENSG00000286610 ENST00000783245.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.438
• Publications: 7 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.359 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376360	NR_131187.1	n.162+47899A>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286610	ENST00000783245.1	n.1045-32350A>C		intron_variant	Intron 1 of 1
ENSG00000286610	ENST00000783246.1	n.352-9667A>C		intron_variant	Intron 1 of 2
ENSG00000286610	ENST00000783529.1	n.877-37811A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32147 AN: 151980 Hom.: 3571 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.212 AC: 32180 AN: 152100 Hom.: 3586 Cov.: 32 AF XY: 0.219 AC XY: 16251 AN XY: 74332

African (AFR) AF: 0.165 AC: 6851 AN: 41512

American (AMR) AF: 0.274 AC: 4183 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 855 AN: 3470

East Asian (EAS) AF: 0.372 AC: 1924 AN: 5166

South Asian (SAS) AF: 0.246 AC: 1186 AN: 4820

European-Finnish (FIN) AF: 0.261 AC: 2754 AN: 10554

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13739 AN: 67986

Other (OTH) AF: 0.236 AC: 499 AN: 2114

Alfa AF: 0.206 Hom.: 1096

Bravo AF: 0.213

Asia WGS AF: 0.293 AC: 1022 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.64
DANN	Benign	0.34
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs17135159; hg19: chr10-3408947;