14-53623359-T-G

Variant names:

• chr14-53623359-T-G
• rs10483623
• ENST00000456100.6:n.326-63840T>G

Variant summary

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

The ENST00000456100.6(DDHD1-DT):​n.326-63840T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 152,188 control chromosomes in the GnomAD database, including 2,143 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 0.16 (2143 hom., cov: 32)
• Consequence: DDHD1-DT ENST00000456100.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.116
• Publications: 3 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000456100.6. 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	ENST00000456100.6	TSL:4	n.326-63840T>G		intron	N/A
	DDHD1-DT	ENST00000648066.2		n.675-63840T>G		intron	N/A
	DDHD1-DT	ENST00000663444.2		n.617-63840T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24518 AN: 152070 Hom.: 2142 Cov.: 32

Gnomad AFR AF: 0.0961

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.0791

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.161 AC: 24525 AN: 152188 Hom.: 2143 Cov.: 32 AF XY: 0.158 AC XY: 11754 AN XY: 74416

African (AFR) AF: 0.0962 AC: 3994 AN: 41528

American (AMR) AF: 0.125 AC: 1909 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 800 AN: 3472

East Asian (EAS) AF: 0.0793 AC: 411 AN: 5186

South Asian (SAS) AF: 0.167 AC: 807 AN: 4828

European-Finnish (FIN) AF: 0.167 AC: 1766 AN: 10598

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 14027 AN: 67986

Other (OTH) AF: 0.180 AC: 379 AN: 2110

Alfa AF: 0.195 Hom.: 1646

Bravo AF: 0.156

Asia WGS AF: 0.109 AC: 380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.95
DANN	Benign	0.31
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs10483623; hg19: chr14-54090077;