rs12434047

chr14-53370767-G-Achr14-53370767-G-Cchr14-53370767-G-T

Variant summary

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

The ENST00000648066.1(ENSG00000237356):n.334+1266G>A 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 0.243 in 151,628 control chromosomes in the GnomAD database, including 4,886 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 0.24 (4886 hom., cov: 31)
• Consequence: ENST00000648066.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.480

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370504	XR_943876.3	n.29700+1266G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000648066.1	n.334+1266G>A		intron_variant, non_coding_transcript_variant
	ENST00000652780.1	n.42-5507C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36871 AN: 151510 Hom.: 4891 Cov.: 31

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.243 AC: 36884 AN: 151628 Hom.: 4886 Cov.: 31 AF XY: 0.250 AC XY: 18500 AN XY: 74094

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.262

Gnomad4 EAS AF: 0.479

Gnomad4 SAS AF: 0.368

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.238

Alfa AF: 0.252 Hom.: 8184

Bravo AF: 0.239

Asia WGS AF: 0.395 AC: 1375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
Cadd	Benign	0.46
Dann	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12434047; hg19: chr14-53837485;