chr14-53363527-A-G

Variant names:

• chr14-53363527-A-G
• rs10138849
• ENST00000435322.1:n.520-5928A>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.520-5928A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.507 in 151,968 control chromosomes in the GnomAD database, including 19,751 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 0.51 (19751 hom., cov: 31)
• Consequence: DDHD1-DT ENST00000435322.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.225
• Publications: 2 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=-0.65).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.638 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.520-5928A>G		intron	N/A
	DDHD1-DT	ENST00000456100.6	TSL:4	n.276-5925A>G		intron	N/A
	DDHD1-DT	ENST00000648066.2		n.625-5925A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.507 AC: 76944 AN: 151850 Hom.: 19728 Cov.: 31

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.507 AC: 77022 AN: 151968 Hom.: 19751 Cov.: 31 AF XY: 0.513 AC XY: 38128 AN XY: 74292

African (AFR) AF: 0.514 AC: 21281 AN: 41426

American (AMR) AF: 0.543 AC: 8292 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1682 AN: 3470

East Asian (EAS) AF: 0.615 AC: 3172 AN: 5154

South Asian (SAS) AF: 0.657 AC: 3159 AN: 4810

European-Finnish (FIN) AF: 0.507 AC: 5359 AN: 10570

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.478 AC: 32488 AN: 67956

Other (OTH) AF: 0.487 AC: 1027 AN: 2108

Alfa AF: 0.489 Hom.: 3088

Bravo AF: 0.507

Asia WGS AF: 0.607 AC: 2113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	14
DANN	Benign	0.96
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs10138849; hg19: chr14-53830245;