rs7152946

Variant names:

• chr14-53584358-A-C
• rs7152946
• ENST00000456100.6:n.326-102841A>C

Your query was ambiguous. Multiple possible variants found:

• chr14-53584358-A-C
• chr14-53584358-A-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.326-102841A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,226 control chromosomes in the GnomAD database, including 1,721 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 0.15 (1721 hom., cov: 32)
• Consequence: DDHD1-DT ENST00000456100.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.828
• Publications: 5 publications found

Genes affected

DDHD1-DT (HGNC:55441): (DDHD1 divergent transcript)

ENSG00000225680 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.163 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.326-102841A>C		intron	N/A
	DDHD1-DT	ENST00000648066.2		n.675-102841A>C		intron	N/A
	DDHD1-DT	ENST00000655713.1		n.439-6777A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22615 AN: 152108 Hom.: 1719 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.0857

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.149 AC: 22631 AN: 152226 Hom.: 1721 Cov.: 32 AF XY: 0.147 AC XY: 10936 AN XY: 74414

African (AFR) AF: 0.166 AC: 6913 AN: 41522

American (AMR) AF: 0.142 AC: 2167 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 514 AN: 3470

East Asian (EAS) AF: 0.135 AC: 699 AN: 5182

South Asian (SAS) AF: 0.0848 AC: 409 AN: 4824

European-Finnish (FIN) AF: 0.137 AC: 1458 AN: 10610

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 10013 AN: 68006

Other (OTH) AF: 0.143 AC: 302 AN: 2112

Alfa AF: 0.147 Hom.: 2975

Bravo AF: 0.151

Asia WGS AF: 0.135 AC: 470 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.7
DANN	Benign	0.63
PhyloP100		0.83

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: rs7152946;

hg19: chr14-54051076;