14-53337411-T-C

Variant names:

• chr14-53337411-T-C
• rs4901408
• XR_001750975.3:n.16760T>C

Variant summary

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

The XR_001750975.3(LOC105370504):​n.16760T>C 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 0.532 in 151,980 control chromosomes in the GnomAD database, including 21,768 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 0.53 (21768 hom., cov: 32)
• Consequence: LOC105370504 XR_001750975.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 6 publications found

Genes affected

LOC105370504 (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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.641 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370504	XR_001750975.3	n.16760T>C		non_coding_transcript_exon_variant	Exon 1 of 3
LOC105370504	XR_007064173.1	n.16760T>C		non_coding_transcript_exon_variant	Exon 1 of 3
LOC105370504	XR_007064175.1	n.16760T>C		non_coding_transcript_exon_variant	Exon 1 of 5
LOC105370504	XR_943876.3	n.16760T>C		non_coding_transcript_exon_variant	Exon 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DDHD1-DT	ENST00000435322.1	n.519+19273T>C		intron_variant	Intron 3 of 3	4
DDHD1-DT	ENST00000456100.6	n.275+19273T>C		intron_variant	Intron 2 of 3	4
DDHD1-DT	ENST00000648066.2	n.624+19273T>C		intron_variant	Intron 3 of 9

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80753 AN: 151862 Hom.: 21735 Cov.: 32

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.532 AC: 80848 AN: 151980 Hom.: 21768 Cov.: 32 AF XY: 0.536 AC XY: 39798 AN XY: 74272

African (AFR) AF: 0.597 AC: 24738 AN: 41454

American (AMR) AF: 0.547 AC: 8362 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.474 AC: 1642 AN: 3466

East Asian (EAS) AF: 0.627 AC: 3225 AN: 5146

South Asian (SAS) AF: 0.660 AC: 3181 AN: 4822

European-Finnish (FIN) AF: 0.509 AC: 5361 AN: 10540

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.481 AC: 32697 AN: 67954

Other (OTH) AF: 0.504 AC: 1065 AN: 2114

Alfa AF: 0.483 Hom.: 9512

Bravo AF: 0.536

Asia WGS AF: 0.632 AC: 2198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.0050
DANN	Benign	0.20
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs4901408; hg19: chr14-53804129;