14-53606140-C-T

Variant names:

• chr14-53606140-C-T
• rs1380131
• XR_007064176.1:n.4943G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007064176.1(LOC124903316):​n.4943G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0785 in 152,244 control chromosomes in the GnomAD database, including 694 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 0.079 (694 hom., cov: 33)
• Consequence: LOC124903316 XR_007064176.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.626
• Publications: 11 publications found

Genes affected

LOC124903316 (HGNC:):

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903316	XR_007064176.1	n.4943G>A		non_coding_transcript_exon_variant	Exon 2 of 2
LOC105370504	XR_001750974.1	n.3896-81059C>T		intron_variant	Intron 2 of 2
LOC105370504	XR_001750975.3	n.29701-81059C>T		intron_variant	Intron 2 of 2
LOC105370504	XR_943876.3	n.29701-81059C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000225680	ENST00000436530.1	n.375-5957G>A		intron_variant	Intron 1 of 1	3
DDHD1-DT	ENST00000456100.6	n.326-81059C>T		intron_variant	Intron 3 of 3	4
DDHD1-DT	ENST00000648066.2	n.675-81059C>T		intron_variant	Intron 4 of 9

Frequencies

GnomAD3 genomes AF: 0.0784 AC: 11929 AN: 152130 Hom.: 684 Cov.: 33

Gnomad AFR AF: 0.0231

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.0996

Gnomad ASJ AF: 0.0726

Gnomad EAS AF: 0.0898

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.0867

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0924

Gnomad OTH AF: 0.0692

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

GnomAD4 genome AF: 0.0785 AC: 11954 AN: 152244 Hom.: 694 Cov.: 33 AF XY: 0.0818 AC XY: 6091 AN XY: 74440

African (AFR) AF: 0.0231 AC: 959 AN: 41554

American (AMR) AF: 0.101 AC: 1538 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0726 AC: 252 AN: 3470

East Asian (EAS) AF: 0.0900 AC: 466 AN: 5180

South Asian (SAS) AF: 0.264 AC: 1274 AN: 4820

European-Finnish (FIN) AF: 0.0867 AC: 918 AN: 10594

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0924 AC: 6286 AN: 68020

Other (OTH) AF: 0.0747 AC: 157 AN: 2102

Alfa AF: 0.0927 Hom.: 2542

Bravo AF: 0.0740

Asia WGS AF: 0.177 AC: 614 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.56
DANN	Benign	0.59
PhyloP100		-0.63
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs1380131; hg19: chr14-54072858;