ENST00000653925.1:n.38-960C>T

Variant names:

• chr4-33201720-C-T
• rs10517273
• ENST00000653925.1:n.38-960C>T

Variant summary

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

The ENST00000653925.1(ENSG00000287968):​n.38-960C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0589 in 152,024 control chromosomes in the GnomAD database, including 587 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 0.059 (587 hom., cov: 32)
• Consequence: ENSG00000287968 ENST00000653925.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.501
• Publications: 0 publications found

Genes affected

ENSG00000287968 (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 (AFR) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287968	ENST00000653925.1	n.38-960C>T		intron_variant	Intron 1 of 2
ENSG00000287968	ENST00000795184.1	n.419-12649C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0588 AC: 8931 AN: 151908 Hom.: 581 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0214

Gnomad ASJ AF: 0.0110

Gnomad EAS AF: 0.0164

Gnomad SAS AF: 0.0327

Gnomad FIN AF: 0.0231

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0162

Gnomad OTH AF: 0.0411

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

GnomAD4 genome AF: 0.0589 AC: 8959 AN: 152024 Hom.: 587 Cov.: 32 AF XY: 0.0573 AC XY: 4260 AN XY: 74314

African (AFR) AF: 0.166 AC: 6895 AN: 41414

American (AMR) AF: 0.0214 AC: 327 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0110 AC: 38 AN: 3470

East Asian (EAS) AF: 0.0162 AC: 84 AN: 5170

South Asian (SAS) AF: 0.0322 AC: 155 AN: 4820

European-Finnish (FIN) AF: 0.0231 AC: 244 AN: 10572

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0162 AC: 1104 AN: 67982

Other (OTH) AF: 0.0402 AC: 85 AN: 2114

Alfa AF: 0.0328 Hom.: 152

Bravo AF: 0.0641

Asia WGS AF: 0.0330 AC: 114 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	2.5
DANN	Benign	0.69
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs10517273; hg19: chr4-33203342;