rs7156227

Variant names:

• chr14-53588619-A-G
• rs7156227
• ENST00000456100.6:n.326-98580A>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.326-98580A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 152,056 control chromosomes in the GnomAD database, including 9,377 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 0.35 (9377 hom., cov: 32)
• Consequence: DDHD1-DT ENST00000456100.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.120
• Publications: 4 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.422 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.326-98580A>G		intron	N/A
	DDHD1-DT	ENST00000648066.2		n.675-98580A>G		intron	N/A
	DDHD1-DT	ENST00000655713.1		n.439-2516A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.349 AC: 53016 AN: 151938 Hom.: 9354 Cov.: 32

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.349 AC: 53081 AN: 152056 Hom.: 9377 Cov.: 32 AF XY: 0.346 AC XY: 25697 AN XY: 74318

African (AFR) AF: 0.427 AC: 17684 AN: 41434

American (AMR) AF: 0.333 AC: 5090 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1103 AN: 3470

East Asian (EAS) AF: 0.221 AC: 1145 AN: 5182

South Asian (SAS) AF: 0.399 AC: 1928 AN: 4830

European-Finnish (FIN) AF: 0.281 AC: 2969 AN: 10554

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.327 AC: 22199 AN: 67978

Other (OTH) AF: 0.327 AC: 691 AN: 2114

Alfa AF: 0.338 Hom.: 38206

Bravo AF: 0.356

Asia WGS AF: 0.337 AC: 1173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.7
DANN	Benign	0.63
PhyloP100		0.12

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: rs7156227;

hg19: chr14-54055337;