ENST00000644129.1:n.282-58382G>C

Variant names:

• chr6-105737873-C-G
• rs2895615
• ENST00000644129.1:n.282-58382G>C

Variant summary

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

The ENST00000644129.1(ENSG00000284999):​n.282-58382G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.709 in 151,910 control chromosomes in the GnomAD database, including 38,295 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 0.71 (38295 hom., cov: 31)
• Consequence: ENSG00000284999 ENST00000644129.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.962
• Publications: 1 publications found

Genes affected

ENSG00000284999 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.749 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
ENSG00000284999	ENST00000644129.1	n.282-58382G>C		intron_variant	Intron 3 of 3
ENSG00000297802	ENST00000751008.1	n.463-3244C>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.708 AC: 107544 AN: 151792 Hom.: 38250 Cov.: 31

Gnomad AFR AF: 0.756

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.730

Gnomad SAS AF: 0.723

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.656

Gnomad NFE AF: 0.676

Gnomad OTH AF: 0.700

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

GnomAD4 genome AF: 0.709 AC: 107642 AN: 151910 Hom.: 38295 Cov.: 31 AF XY: 0.708 AC XY: 52541 AN XY: 74232

African (AFR) AF: 0.756 AC: 31336 AN: 41440

American (AMR) AF: 0.757 AC: 11542 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2377 AN: 3466

East Asian (EAS) AF: 0.730 AC: 3768 AN: 5162

South Asian (SAS) AF: 0.723 AC: 3476 AN: 4808

European-Finnish (FIN) AF: 0.664 AC: 7007 AN: 10550

Middle Eastern (MID) AF: 0.661 AC: 193 AN: 292

European-Non Finnish (NFE) AF: 0.676 AC: 45950 AN: 67936

Other (OTH) AF: 0.704 AC: 1480 AN: 2102

Alfa AF: 0.560 Hom.: 1202

Bravo AF: 0.716

Asia WGS AF: 0.753 AC: 2622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.34
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs2895615; hg19: chr6-106185748;