chr12-17114421-T-C

Position:

• chr12-17114421-T-C

Variant summary

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

The ENST00000649143.1(ENSG00000285724):​n.901+14571A>G variant causes a intron, non coding transcript 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: ENST00000649143.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.355

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000649143.1	n.901+14571A>G		intron_variant, non_coding_transcript_variant
	ENST00000671686.1	n.507+14571A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.521

Gnomad4 AMR AF: 0.588

Gnomad4 ASJ AF: 0.548

Gnomad4 EAS AF: 0.755

Gnomad4 SAS AF: 0.691

Gnomad4 FIN AF: 0.579

Gnomad4 NFE AF: 0.509

Gnomad4 OTH AF: 0.538

Alfa AF: 0.510 Hom.: 2880

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7133213; hg19: chr12-17267355;