rs12431592

Positions:

• chr14-56677522-G-C

Variant summary

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

The ENST00000554597.5(ENSG00000259133):​n.370-28394C>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 0.494 in 152,100 control chromosomes in the GnomAD database, including 21,936 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 0.49 (21936 hom., cov: 32)
• Consequence: ENST00000554597.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.409

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.632 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
	ENST00000554597.5	n.370-28394C>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.495 AC: 75180 AN: 151982 Hom.: 21926 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.723

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.494 AC: 75202 AN: 152100 Hom.: 21936 Cov.: 32 AF XY: 0.499 AC XY: 37129 AN XY: 74360

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.524

Gnomad4 ASJ AF: 0.541

Gnomad4 EAS AF: 0.650

Gnomad4 SAS AF: 0.561

Gnomad4 FIN AF: 0.678

Gnomad4 NFE AF: 0.637

Gnomad4 OTH AF: 0.513

Alfa AF: 0.554 Hom.: 3164

Bravo AF: 0.472

Asia WGS AF: 0.592 AC: 2056 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12431592; hg19: chr14-57144240;