rs12819505

Variant names:

• chr12-1647499-A-G
• rs12819505
• ENST00000728335.1:n.105-696T>C

Variant summary

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

The ENST00000728335.1(ENSG00000289832):​n.105-696T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0479 in 152,248 control chromosomes in the GnomAD database, including 253 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 0.048 (253 hom., cov: 32)
• Consequence: ENSG00000289832 ENST00000728335.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.200
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0685 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.105-696T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0480 AC: 7302 AN: 152128 Hom.: 253 Cov.: 32

Gnomad AFR AF: 0.0120

Gnomad AMI AF: 0.0648

Gnomad AMR AF: 0.0399

Gnomad ASJ AF: 0.0588

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0168

Gnomad FIN AF: 0.0899

Gnomad MID AF: 0.0318

Gnomad NFE AF: 0.0701

Gnomad OTH AF: 0.0545

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

GnomAD4 genome AF: 0.0479 AC: 7299 AN: 152248 Hom.: 253 Cov.: 32 AF XY: 0.0472 AC XY: 3511 AN XY: 74432

African (AFR) AF: 0.0120 AC: 498 AN: 41546

American (AMR) AF: 0.0399 AC: 610 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0588 AC: 204 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5174

South Asian (SAS) AF: 0.0164 AC: 79 AN: 4812

European-Finnish (FIN) AF: 0.0899 AC: 954 AN: 10616

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0701 AC: 4771 AN: 68012

Other (OTH) AF: 0.0540 AC: 114 AN: 2112

Alfa AF: 0.0616 Hom.: 412

Bravo AF: 0.0416

Asia WGS AF: 0.00779 AC: 27 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	2.4
DANN	Benign	0.38
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs12819505; hg19: chr12-1756665;