14-53363527-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370504	XR_001750975.3	n.29651-5925A>G		intron_variant	Intron 1 of 2
LOC105370504	XR_007064173.1	n.29651-5925A>G		intron_variant	Intron 1 of 2
LOC105370504	XR_007064175.1	n.29651-5925A>G		intron_variant	Intron 1 of 4
LOC105370504	XR_943876.3	n.29651-5925A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DDHD1-DT	ENST00000435322.1	n.520-5928A>G		intron_variant	Intron 3 of 3	4
DDHD1-DT	ENST00000456100.6	n.276-5925A>G		intron_variant	Intron 2 of 3	4
DDHD1-DT	ENST00000648066.2	n.625-5925A>G		intron_variant	Intron 3 of 9

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 v4.3

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;