chr12-1647476-C-A

Variant names:

• chr12-1647476-C-A
• rs2010851
• ENST00000728335.1:n.105-673G>T

Variant summary

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

The ENST00000728335.1(ENSG00000289832):​n.105-673G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.674 in 152,006 control chromosomes in the GnomAD database, including 34,634 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 0.67 (34634 hom., cov: 32)
• Consequence: ENSG00000289832 ENST00000728335.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.650
• Publications: 12 publications found

Genes affected

ENSG00000289832 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.696 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
ENSG00000289832	ENST00000728335.1	n.105-673G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.674 AC: 102361 AN: 151888 Hom.: 34623 Cov.: 32

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.674 AC: 102424 AN: 152006 Hom.: 34634 Cov.: 32 AF XY: 0.677 AC XY: 50343 AN XY: 74318

African (AFR) AF: 0.607 AC: 25157 AN: 41426

American (AMR) AF: 0.707 AC: 10796 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 2101 AN: 3472

East Asian (EAS) AF: 0.706 AC: 3647 AN: 5166

South Asian (SAS) AF: 0.688 AC: 3317 AN: 4824

European-Finnish (FIN) AF: 0.759 AC: 8039 AN: 10588

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.695 AC: 47219 AN: 67952

Other (OTH) AF: 0.654 AC: 1376 AN: 2104

Alfa AF: 0.680 Hom.: 134535

Bravo AF: 0.665

Asia WGS AF: 0.675 AC: 2349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.53
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs2010851; hg19: chr12-1756642;