rs1704754

Variant names:

• chr1-162790761-C-G
• rs1704754
• NM_016371.4:c.-40C>G

Your query was ambiguous. Multiple possible variants found:

• chr1-162790761-C-G
• chr1-162790761-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_016371.4(HSD17B7):​c.-40C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 26)
  • Exomes 𝑓: 8.6e-7 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: HSD17B7 NM_016371.4 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98
• Publications: 10 publications found

Genes affected

HSD17B7 (HGNC:5215): (hydroxysteroid 17-beta dehydrogenase 7) HSD17B7 encodes an enzyme that functions both as a 17-beta-hydroxysteroid dehydrogenase (EC 1.1.1.62) in the biosynthesis of sex steroids and as a 3-ketosteroid reductase (EC 1.1.1.270) in the biosynthesis of cholesterol (Marijanovic et al., 2003 [PubMed 12829805]).[supplied by OMIM, May 2010]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016371.4. 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
	HSD17B7	NM_016371.4	MANE Select	c.-40C>G		5_prime_UTR	Exon 1 of 9	NP_057455.1
	HSD17B7	NM_001304512.2		c.-40C>G		5_prime_UTR	Exon 1 of 4	NP_001291441.1
	HSD17B7	NM_001304513.2		c.-40C>G		5_prime_UTR	Exon 1 of 4	NP_001291442.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HSD17B7	ENST00000254521.8	TSL:1 MANE Select	c.-40C>G		5_prime_UTR	Exon 1 of 9	ENSP00000254521.3
	HSD17B7	ENST00000463037.5	TSL:3	n.41C>G		non_coding_transcript_exon	Exon 1 of 6
	HSD17B7	ENST00000466176.5	TSL:3	n.-40C>G		non_coding_transcript_exon	Exon 1 of 6	ENSP00000436334.1

Frequencies

GnomAD3 genomes Cov.: 26

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 8.63e-7 AC: 1 AN: 1158264 Hom.: 0 Cov.: 16 AF XY: 0.00 AC XY: 0 AN XY: 586870

African (AFR) AF: 0.00 AC: 0 AN: 28168

American (AMR) AF: 0.00 AC: 0 AN: 40740

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 23950

East Asian (EAS) AF: 0.00 AC: 0 AN: 36584

South Asian (SAS) AF: 0.00 AC: 0 AN: 76076

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 51306

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5194

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 845968

Other (OTH) AF: 0.0000199 AC: 1 AN: 50278

GnomAD4 genome Cov.: 26

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.90
DANN	Benign	0.48
PhyloP100		-2.0
PromoterAI		-0.13	Neutral

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: rs1704754; hg19: chr1-162760551;