12-17114421-T-C

Variant names:

• chr12-17114421-T-C
• rs7133213
• ENST00000649143.1:n.901+14571A>G

Variant summary

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

The ENST00000649143.1(ENSG00000285724):​n.901+14571A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.54 in 151,706 control chromosomes in the GnomAD database, including 22,486 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 (22486 hom., cov: 31)
• Consequence: ENSG00000285724 ENST00000649143.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.355
• Publications: 2 publications found

Genes affected

ENSG00000285724 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.735 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+14571A>G		intron_variant	Intron 6 of 6
ENSG00000285724	ENST00000671686.1	n.507+14571A>G		intron_variant	Intron 4 of 4
ENSG00000287455	ENST00000792895.1	n.216-29762T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.540 AC: 81849 AN: 151588 Hom.: 22466 Cov.: 31

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.692

Gnomad FIN AF: 0.579

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.540 AC: 81913 AN: 151706 Hom.: 22486 Cov.: 31 AF XY: 0.546 AC XY: 40449 AN XY: 74116

African (AFR) AF: 0.521 AC: 21577 AN: 41414

American (AMR) AF: 0.588 AC: 8966 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 1899 AN: 3466

East Asian (EAS) AF: 0.755 AC: 3871 AN: 5130

South Asian (SAS) AF: 0.691 AC: 3331 AN: 4820

European-Finnish (FIN) AF: 0.579 AC: 6093 AN: 10516

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.509 AC: 34509 AN: 67804

Other (OTH) AF: 0.538 AC: 1133 AN: 2106

Alfa AF: 0.511 Hom.: 2985

Bravo AF: 0.538

Asia WGS AF: 0.732 AC: 2545 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.7
DANN	Benign	0.58
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs7133213; hg19: chr12-17267355;