14-53353259-A-G

Variant names:

• chr14-53353259-A-G
• rs1255309
• ENST00000435322.1:n.520-16196A>G

Variant summary

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

The ENST00000435322.1(DDHD1-DT):​n.520-16196A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.866 in 152,206 control chromosomes in the GnomAD database, including 57,686 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 0.87 (57686 hom., cov: 32)
• Consequence: DDHD1-DT ENST00000435322.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.120
• Publications: 4 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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.924 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000435322.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DDHD1-DT	ENST00000435322.1	TSL:4	n.520-16196A>G		intron	N/A
	DDHD1-DT	ENST00000456100.6	TSL:4	n.276-16193A>G		intron	N/A
	DDHD1-DT	ENST00000648066.2		n.625-16193A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.866 AC: 131690 AN: 152088 Hom.: 57669 Cov.: 32

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.956

Gnomad AMR AF: 0.885

Gnomad ASJ AF: 0.922

Gnomad EAS AF: 0.850

Gnomad SAS AF: 0.895

Gnomad FIN AF: 0.952

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.930

Gnomad OTH AF: 0.882

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

GnomAD4 genome AF: 0.866 AC: 131761 AN: 152206 Hom.: 57686 Cov.: 32 AF XY: 0.868 AC XY: 64606 AN XY: 74424

African (AFR) AF: 0.722 AC: 29956 AN: 41492

American (AMR) AF: 0.885 AC: 13542 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.922 AC: 3200 AN: 3472

East Asian (EAS) AF: 0.850 AC: 4391 AN: 5164

South Asian (SAS) AF: 0.894 AC: 4313 AN: 4822

European-Finnish (FIN) AF: 0.952 AC: 10106 AN: 10610

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.930 AC: 63253 AN: 68024

Other (OTH) AF: 0.881 AC: 1865 AN: 2116

Alfa AF: 0.915 Hom.: 30563

Bravo AF: 0.854

Asia WGS AF: 0.846 AC: 2943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.2
DANN	Benign	0.76
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs1255309; hg19: chr14-53819977;