ENST00000654305.2:n.104-667C>T

Variant names:

• chr10-18746022-C-T
• rs10763625
• ENST00000654305.2:n.104-667C>T

Variant summary

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

The ENST00000654305.2(ENSG00000234244):​n.104-667C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 152,132 control chromosomes in the GnomAD database, including 2,369 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 0.17 (2369 hom., cov: 32)
• Consequence: ENSG00000234244 ENST00000654305.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.569
• Publications: 3 publications found

Genes affected

ENSG00000234244 (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 = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376440	XR_930720.2	n.52-32270C>T		intron_variant	Intron 1 of 4
LOC105376440	XR_930721.2	n.69-667C>T		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234244	ENST00000654305.2	n.104-667C>T		intron_variant	Intron 1 of 2
ENSG00000234244	ENST00000654415.1	n.220+623C>T		intron_variant	Intron 3 of 4
ENSG00000234244	ENST00000723466.1	n.54-32270C>T		intron_variant	Intron 1 of 7

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25829 AN: 152014 Hom.: 2367 Cov.: 32

Gnomad AFR AF: 0.0968

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.170 AC: 25840 AN: 152132 Hom.: 2369 Cov.: 32 AF XY: 0.169 AC XY: 12571 AN XY: 74372

African (AFR) AF: 0.0967 AC: 4015 AN: 41538

American (AMR) AF: 0.166 AC: 2537 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 727 AN: 3470

East Asian (EAS) AF: 0.212 AC: 1096 AN: 5174

South Asian (SAS) AF: 0.134 AC: 646 AN: 4826

European-Finnish (FIN) AF: 0.201 AC: 2125 AN: 10554

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.207 AC: 14064 AN: 67972

Other (OTH) AF: 0.164 AC: 346 AN: 2112

Alfa AF: 0.193 Hom.: 4735

Bravo AF: 0.164

Asia WGS AF: 0.179 AC: 620 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.32
DANN	Benign	0.16
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs10763625; hg19: chr10-19034951;