NM_015510.5:c.619+564T>C

Variant names:

• chr17-21185027-T-C
• rs1448
• NM_015510.5:c.619+564T>C

Variant summary

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

The NM_015510.5(DHRS7B):​c.619+564T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 152,078 control chromosomes in the GnomAD database, including 7,768 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 0.32 (7768 hom., cov: 33)
• Consequence: DHRS7B NM_015510.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.772
• Publications: 10 publications found

Genes affected

DHRS7B (HGNC:24547): (dehydrogenase/reductase 7B) Predicted to enable DNA-binding transcription factor binding activity and transcription corepressor activity. Predicted to be involved in neutrophil differentiation. Predicted to act upstream of or within several processes, including brown fat cell differentiation; phosphatidylcholine biosynthetic process; and regulation of cold-induced thermogenesis. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015510.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DHRS7B	NM_015510.5	MANE Select	c.619+564T>C		intron	N/A	NP_056325.2
	DHRS7B	NM_001393657.1		c.613+564T>C		intron	N/A	NP_001380586.1
	DHRS7B	NM_001393658.1		c.607+564T>C		intron	N/A	NP_001380587.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DHRS7B	ENST00000395511.8	TSL:1 MANE Select	c.619+564T>C		intron	N/A	ENSP00000378887.3
	DHRS7B	ENST00000346603.4	TSL:1	n.943+564T>C		intron	N/A
	DHRS7B	ENST00000579303.5	TSL:5	c.574+564T>C		intron	N/A	ENSP00000468585.1

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48280 AN: 151960 Hom.: 7765 Cov.: 33

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.318 AC: 48308 AN: 152078 Hom.: 7768 Cov.: 33 AF XY: 0.316 AC XY: 23496 AN XY: 74342

African (AFR) AF: 0.269 AC: 11157 AN: 41480

American (AMR) AF: 0.324 AC: 4942 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 854 AN: 3470

East Asian (EAS) AF: 0.275 AC: 1422 AN: 5178

South Asian (SAS) AF: 0.365 AC: 1762 AN: 4824

European-Finnish (FIN) AF: 0.338 AC: 3571 AN: 10568

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.346 AC: 23510 AN: 67976

Other (OTH) AF: 0.328 AC: 692 AN: 2108

Alfa AF: 0.316 Hom.: 1336

Bravo AF: 0.312

Asia WGS AF: 0.311 AC: 1082 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.0
DANN	Benign	0.87
PhyloP100		-0.77
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1448; hg19: chr17-21088340;