chr1-101075443-T-C

Variant names:

• chr1-101075443-T-C
• rs17450029
• ENST00000449473.2:n.290+49T>C

Variant summary

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

The ENST00000449473.2(DPH5-DT):​n.290+49T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 152,078 control chromosomes in the GnomAD database, including 3,836 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 0.21 (3836 hom., cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: DPH5-DT ENST00000449473.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.480
• Publications: 11 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DPH5-DT	NR_109849.1	n.265T>C		non_coding_transcript_exon_variant	Exon 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DPH5-DT	ENST00000449473.2	n.290+49T>C		intron_variant	Intron 2 of 6	1
DPH5-DT	ENST00000446527.8	n.258T>C		non_coding_transcript_exon_variant	Exon 2 of 5	3
DPH5-DT	ENST00000451213.2	n.267T>C		non_coding_transcript_exon_variant	Exon 2 of 5	2

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32520 AN: 151960 Hom.: 3824 Cov.: 31

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.207

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.214 AC: 32553 AN: 152078 Hom.: 3836 Cov.: 31 AF XY: 0.215 AC XY: 15948 AN XY: 74342

African (AFR) AF: 0.149 AC: 6204 AN: 41520

American (AMR) AF: 0.323 AC: 4922 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 499 AN: 3470

East Asian (EAS) AF: 0.114 AC: 592 AN: 5186

South Asian (SAS) AF: 0.203 AC: 974 AN: 4806

European-Finnish (FIN) AF: 0.236 AC: 2496 AN: 10582

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16246 AN: 67952

Other (OTH) AF: 0.206 AC: 434 AN: 2108

Alfa AF: 0.231 Hom.: 6293

Bravo AF: 0.216

Asia WGS AF: 0.167 AC: 581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.63
DANN	Benign	0.38
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs17450029; hg19: chr1-101540999;