chr14-53678599-T-C

Variant names:

• chr14-53678599-T-C
• rs7146962
• ENST00000456100.6:n.326-8600T>C

Variant summary

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

The ENST00000456100.6(DDHD1-DT):​n.326-8600T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 152,096 control chromosomes in the GnomAD database, including 7,437 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 0.30 (7437 hom., cov: 32)
• Consequence: DDHD1-DT ENST00000456100.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 8 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 (AFR) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370504	XR_001750974.1	n.3896-8600T>C		intron_variant	Intron 2 of 2
LOC105370504	XR_001750975.3	n.29701-8600T>C		intron_variant	Intron 2 of 2
LOC105370504	XR_943876.3	n.29701-8600T>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DDHD1-DT	ENST00000456100.6	n.326-8600T>C		intron_variant	Intron 3 of 3	4
DDHD1-DT	ENST00000648066.2	n.675-8600T>C		intron_variant	Intron 4 of 9
DDHD1-DT	ENST00000663444.2	n.617-8600T>C		intron_variant	Intron 3 of 4
DDHD1-DT	ENST00000669612.1	n.398-8600T>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45644 AN: 151978 Hom.: 7403 Cov.: 32

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.301 AC: 45744 AN: 152096 Hom.: 7437 Cov.: 32 AF XY: 0.296 AC XY: 22006 AN XY: 74352

African (AFR) AF: 0.433 AC: 17973 AN: 41464

American (AMR) AF: 0.295 AC: 4506 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 866 AN: 3472

East Asian (EAS) AF: 0.255 AC: 1317 AN: 5168

South Asian (SAS) AF: 0.256 AC: 1237 AN: 4826

European-Finnish (FIN) AF: 0.186 AC: 1975 AN: 10590

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 16994 AN: 67988

Other (OTH) AF: 0.307 AC: 649 AN: 2112

Alfa AF: 0.264 Hom.: 2972

Bravo AF: 0.317

Asia WGS AF: 0.307 AC: 1067 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.19
DANN	Benign	0.28
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs7146962; hg19: chr14-54145317;