rs12434047

Variant names:

• chr14-53370767-G-A
• rs12434047
• ENST00000425648.1:n.121+1266G>A

Your query was ambiguous. Multiple possible variants found:

• chr14-53370767-G-A
• chr14-53370767-G-C
• chr14-53370767-G-T

Variant summary

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

The ENST00000425648.1(DDHD1-DT):​n.121+1266G>A variant causes a intron 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: DDHD1-DT ENST00000425648.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.480
• Publications: 8 publications found

Genes affected

DDHD1-DT (HGNC:55441): (DDHD1 divergent transcript)

ENSG00000286730 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000425648.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DDHD1-DT	ENST00000425648.1	TSL:4	n.121+1266G>A		intron	N/A
	DDHD1-DT	ENST00000456100.6	TSL:4	n.325+1266G>A		intron	N/A
	DDHD1-DT	ENST00000648066.2		n.674+1266G>A		intron	N/A

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

African (AFR) AF: 0.176 AC: 7223 AN: 41114

American (AMR) AF: 0.248 AC: 3786 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 909 AN: 3470

East Asian (EAS) AF: 0.479 AC: 2457 AN: 5132

South Asian (SAS) AF: 0.368 AC: 1772 AN: 4818

European-Finnish (FIN) AF: 0.303 AC: 3201 AN: 10566

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.247 AC: 16816 AN: 67964

Other (OTH) AF: 0.238 AC: 500 AN: 2100

Alfa AF: 0.250 Hom.: 18576

Bravo AF: 0.239

Asia WGS AF: 0.395 AC: 1375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	0.46
DANN	Benign	0.86
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs12434047; hg19: chr14-53837485;