rs12897470

Positions:

• chr14-40356636-G-A
• chr14-40356636-G-C
• chr14-40356636-G-T

Variant summary

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

The ENST00000652126.1(ENSG00000258526):​n.643-14885G>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 0.448 in 150,680 control chromosomes in the GnomAD database, including 15,849 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 0.45 (15849 hom., cov: 29)
• Consequence: ENST00000652126.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66

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 (NFE) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370462	XR_007064129.1	n.196-14885G>A		intron_variant, non_coding_transcript_variant
LOC105370462	XR_943784.3	n.192-14885G>A		intron_variant, non_coding_transcript_variant
LOC105370462	XR_943785.3	n.729+652G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000652126.1	n.643-14885G>A		intron_variant, non_coding_transcript_variant
	ENST00000553464.2	n.501-29616G>A		intron_variant, non_coding_transcript_variant		5
	ENST00000663500.1	n.481-29616G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.448 AC: 67474 AN: 150574 Hom.: 15838 Cov.: 29

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.448 AC: 67504 AN: 150680 Hom.: 15849 Cov.: 29 AF XY: 0.447 AC XY: 32844 AN XY: 73510

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.486

Gnomad4 ASJ AF: 0.527

Gnomad4 EAS AF: 0.307

Gnomad4 SAS AF: 0.274

Gnomad4 FIN AF: 0.573

Gnomad4 NFE AF: 0.507

Gnomad4 OTH AF: 0.459

Alfa AF: 0.317 Hom.: 864

Bravo AF: 0.438

Asia WGS AF: 0.286 AC: 992 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12897470; hg19: chr14-40825840;