14-53453205-C-G

Variant names:

• chr14-53453205-C-G
• rs12147340
• ENST00000425648.1:n.122-72606C>G

Variant summary

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

The ENST00000425648.1(DDHD1-DT):​n.122-72606C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,142 control chromosomes in the GnomAD database, including 1,979 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 0.15 (1979 hom., cov: 32)
• Consequence: DDHD1-DT ENST00000425648.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360
• Publications: 1 publications found

Genes affected

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

LOC105370504 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370504	XR_001750974.1	n.3895+83704C>G		intron_variant	Intron 2 of 2
LOC105370504	XR_001750975.3	n.29700+83704C>G		intron_variant	Intron 2 of 2
LOC105370504	XR_007064173.1	n.29701-57520C>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DDHD1-DT	ENST00000425648.1	n.122-72606C>G		intron_variant	Intron 1 of 1	4
DDHD1-DT	ENST00000456100.6	n.325+83704C>G		intron_variant	Intron 3 of 3	4
DDHD1-DT	ENST00000648066.2	n.674+83704C>G		intron_variant	Intron 4 of 9

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22621 AN: 152022 Hom.: 1977 Cov.: 32

Gnomad AFR AF: 0.0590

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.143

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.149 AC: 22622 AN: 152142 Hom.: 1979 Cov.: 32 AF XY: 0.149 AC XY: 11084 AN XY: 74388

African (AFR) AF: 0.0589 AC: 2445 AN: 41516

American (AMR) AF: 0.172 AC: 2631 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 540 AN: 3470

East Asian (EAS) AF: 0.234 AC: 1212 AN: 5170

South Asian (SAS) AF: 0.131 AC: 631 AN: 4826

European-Finnish (FIN) AF: 0.174 AC: 1835 AN: 10568

Middle Eastern (MID) AF: 0.147 AC: 43 AN: 292

European-Non Finnish (NFE) AF: 0.187 AC: 12686 AN: 68002

Other (OTH) AF: 0.158 AC: 334 AN: 2116

Alfa AF: 0.0833 Hom.: 112

Bravo AF: 0.147

Asia WGS AF: 0.143 AC: 501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.5
DANN	Benign	0.64
PhyloP100		0.036

Splicing

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

Other links and lift over

dbSNP: rs12147340; hg19: chr14-53919923;