15-49624219-C-G

Variant names:

• chr15-49624219-C-G
• rs11070711
• NM_001144955.2:c.-55-894C>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001144955.2(DTWD1):​c.-55-894C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.9 in 152,212 control chromosomes in the GnomAD database, including 62,775 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 0.90 (62775 hom., cov: 32)
• Consequence: DTWD1 NM_001144955.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133

Genes affected

DTWD1 (HGNC:30926): (DTW domain containing 1) Enables tRNA-uridine aminocarboxypropyltransferase activity. Involved in tRNA modification. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DTWD1	NM_001144955.2	c.-55-894C>G		intron_variant	Intron 1 of 4	ENST00000403028.8	NP_001138427.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DTWD1	ENST00000403028.8	c.-55-894C>G		intron_variant	Intron 1 of 4	1	NM_001144955.2	ENSP00000385399.3

Frequencies

GnomAD3 genomes AF: 0.900 AC: 136879 AN: 152094 Hom.: 62733 Cov.: 32

Gnomad AFR AF: 0.701

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.955

Gnomad ASJ AF: 0.986

Gnomad EAS AF: 0.985

Gnomad SAS AF: 0.926

Gnomad FIN AF: 0.982

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.981

Gnomad OTH AF: 0.921

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

GnomAD4 genome AF: 0.900 AC: 136981 AN: 152212 Hom.: 62775 Cov.: 32 AF XY: 0.902 AC XY: 67107 AN XY: 74394

Gnomad4 AFR AF: 0.702

Gnomad4 AMR AF: 0.956

Gnomad4 ASJ AF: 0.986

Gnomad4 EAS AF: 0.985

Gnomad4 SAS AF: 0.926

Gnomad4 FIN AF: 0.982

Gnomad4 NFE AF: 0.981

Gnomad4 OTH AF: 0.922

Alfa AF: 0.934 Hom.: 3333

Bravo AF: 0.891

Asia WGS AF: 0.925 AC: 3216 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.51
DANN	Benign	0.42

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs11070711; hg19: chr15-49916416;