dbSNP rs12147340: DDHD1-DT:n.122-72606C>A (chr14-53453205-C-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000425648.1(DDHD1-DT):n.122-72606C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)

Consequence

DDHD1-DT
ENST00000425648.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0360

Publications

1 publications found

Variant links:

Genes affected

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

DDHD1-DT links:

LOC105370504 (HGNC:):

LOC105370504 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC105370504	XR_001750974.1 link	n.3895+83704C>A	intron_variant	Intron 2 of 2
LOC105370504	XR_001750975.3 link	n.29700+83704C>A	intron_variant	Intron 2 of 2
LOC105370504	XR_007064173.1 link	n.29701-57520C>A	intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
DDHD1-DT	ENST00000425648.1 link	n.122-72606C>A	intron_variant	Intron 1 of 1	4
DDHD1-DT	ENST00000456100.6 link	n.325+83704C>A	intron_variant	Intron 3 of 3	4
DDHD1-DT	ENST00000648066.2 link	n.674+83704C>A	intron_variant	Intron 4 of 9

Frequencies

GnomAD3 genomes

Cov.:

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

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

112

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

4.4

(source)

DANN

Benign

0.70

PhyloP100

0.036

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over