rs7146962

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.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DDHD1-DT	ENST00000456100.6	TSL:4	n.326-8600T>C		intron	N/A
	DDHD1-DT	ENST00000648066.2		n.675-8600T>C		intron	N/A
	DDHD1-DT	ENST00000663444.2		n.617-8600T>C		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7146962;

hg19: chr14-54145317;