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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370504	XR_001750974.1	n.3896-98580A>G		intron_variant	Intron 2 of 2
LOC105370504	XR_001750975.3	n.29701-98580A>G		intron_variant	Intron 2 of 2
LOC105370504	XR_943876.3	n.29701-98580A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DDHD1-DT	ENST00000456100.6	n.326-98580A>G		intron_variant	Intron 3 of 3	4
DDHD1-DT	ENST00000648066.2	n.675-98580A>G		intron_variant	Intron 4 of 9
DDHD1-DT	ENST00000655713.1	n.439-2516A>G		intron_variant	Intron 4 of 4

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 v4.3

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

Other links and lift over

dbSNP: rs7156227; hg19: chr14-54055337;