rs6572915

Variant names:

• chr14-53587721-A-G
• rs6572915
• ENST00000456100.6:n.326-99478A>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.326-99478A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 151,998 control chromosomes in the GnomAD database, including 9,020 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 0.34 (9020 hom., cov: 31)
• Consequence: DDHD1-DT ENST00000456100.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04
• Publications: 2 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.407 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.326-99478A>G		intron	N/A
	DDHD1-DT	ENST00000648066.2		n.675-99478A>G		intron	N/A
	DDHD1-DT	ENST00000655713.1		n.439-3414A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.343 AC: 52035 AN: 151880 Hom.: 8997 Cov.: 31

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.343 AC: 52100 AN: 151998 Hom.: 9020 Cov.: 31 AF XY: 0.340 AC XY: 25243 AN XY: 74316

African (AFR) AF: 0.412 AC: 17067 AN: 41444

American (AMR) AF: 0.326 AC: 4968 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1100 AN: 3464

East Asian (EAS) AF: 0.220 AC: 1140 AN: 5174

South Asian (SAS) AF: 0.397 AC: 1913 AN: 4814

European-Finnish (FIN) AF: 0.280 AC: 2961 AN: 10562

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 21997 AN: 67960

Other (OTH) AF: 0.324 AC: 684 AN: 2114

Alfa AF: 0.334 Hom.: 1074

Bravo AF: 0.349

Asia WGS AF: 0.338 AC: 1175 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.077
DANN	Benign	0.53
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs6572915; hg19: chr14-54054439;