12-17111403-T-C

Variant names:

• chr12-17111403-T-C
• rs7305646
• ENST00000649143.1:n.901+17589A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000649143.1(ENSG00000285724):​n.901+17589A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.539 in 151,858 control chromosomes in the GnomAD database, including 22,456 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 0.54 (22456 hom., cov: 32)
• Consequence: ENSG00000285724 ENST00000649143.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430

Genes affected

ENSG00000285724 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.734 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
ENSG00000285724	ENST00000649143.1	n.901+17589A>G		intron_variant	Intron 6 of 6
ENSG00000285724	ENST00000671686.1	n.507+17589A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81804 AN: 151740 Hom.: 22436 Cov.: 32

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.539 AC: 81868 AN: 151858 Hom.: 22456 Cov.: 32 AF XY: 0.545 AC XY: 40438 AN XY: 74218

Gnomad4 AFR AF: 0.520

Gnomad4 AMR AF: 0.588

Gnomad4 ASJ AF: 0.548

Gnomad4 EAS AF: 0.754

Gnomad4 SAS AF: 0.692

Gnomad4 FIN AF: 0.578

Gnomad4 NFE AF: 0.508

Gnomad4 OTH AF: 0.538

Alfa AF: 0.519 Hom.: 34138

Bravo AF: 0.537

Asia WGS AF: 0.733 AC: 2547 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	3.2
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7305646; hg19: chr12-17264337;