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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370504	XR_001750974.1	n.3895+1266G>A		intron_variant	Intron 2 of 2
LOC105370504	XR_001750975.3	n.29700+1266G>A		intron_variant	Intron 2 of 2
LOC105370504	XR_007064173.1	n.29700+1266G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DDHD1-DT	ENST00000425648.1	n.121+1266G>A		intron_variant	Intron 1 of 1	4
DDHD1-DT	ENST00000456100.6	n.325+1266G>A		intron_variant	Intron 3 of 3	4
DDHD1-DT	ENST00000648066.2	n.674+1266G>A		intron_variant	Intron 4 of 9

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 v4.3

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;