rs12897470

Variant names:

• chr14-40356636-G-A
• rs12897470
• ENST00000553464.2:n.501-29616G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000553464.2(ENSG00000258526):​n.501-29616G>A variant causes a intron 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: ENSG00000258526 ENST00000553464.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66
• Publications: 2 publications found

Genes affected

ENSG00000258526 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000553464.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000258526	ENST00000553464.2	TSL:5	n.501-29616G>A		intron	N/A
	ENSG00000258526	ENST00000652126.1		n.643-14885G>A		intron	N/A
	ENSG00000258526	ENST00000663500.1		n.481-29616G>A		intron	N/A

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

African (AFR) AF: 0.334 AC: 13691 AN: 41040

American (AMR) AF: 0.486 AC: 7368 AN: 15152

Ashkenazi Jewish (ASJ) AF: 0.527 AC: 1826 AN: 3462

East Asian (EAS) AF: 0.307 AC: 1572 AN: 5118

South Asian (SAS) AF: 0.274 AC: 1313 AN: 4786

European-Finnish (FIN) AF: 0.573 AC: 5840 AN: 10192

Middle Eastern (MID) AF: 0.482 AC: 137 AN: 284

European-Non Finnish (NFE) AF: 0.507 AC: 34262 AN: 67636

Other (OTH) AF: 0.459 AC: 962 AN: 2098

Alfa AF: 0.319 Hom.: 915

Bravo AF: 0.438

Asia WGS AF: 0.286 AC: 992 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.37
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs12897470; hg19: chr14-40825840;