rs17410015

chr1-101086370-T-C

Variant summary

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

The NR_109849.1(DPH5-DT):n.799-482T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0608 in 152,254 control chromosomes in the GnomAD database, including 381 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 0.061 (381 hom., cov: 32)
• Consequence: DPH5-DT NR_109849.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.230

Genes affected

DPH5-DT (HGNC:53720): (DPH5 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0859 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DPH5-DT	NR_109849.1	n.799-482T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DPH5-DT	ENST00000659528.3	n.331-482T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0608 AC: 9251 AN: 152136 Hom.: 379 Cov.: 32

Gnomad AFR AF: 0.0178

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.0704

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.0244

Gnomad SAS AF: 0.0348

Gnomad FIN AF: 0.0438

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0878

Gnomad OTH AF: 0.0822

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

GnomAD4 genome AF: 0.0608 AC: 9251 AN: 152254 Hom.: 381 Cov.: 32 AF XY: 0.0581 AC XY: 4324 AN XY: 74446

Gnomad4 AFR AF: 0.0177

Gnomad4 AMR AF: 0.0702

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.0249

Gnomad4 SAS AF: 0.0350

Gnomad4 FIN AF: 0.0438

Gnomad4 NFE AF: 0.0878

Gnomad4 OTH AF: 0.0818

Alfa AF: 0.0857 Hom.: 1228

Bravo AF: 0.0609

Asia WGS AF: 0.0480 AC: 170 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	5.5
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17410015; hg19: chr1-101551926;