rs2804672

Variant names:

• chr10-38367959-G-A
• rs2804672
• ENST00000494540.6:n.742-1994G>A

Variant summary

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

The ENST00000494540.6(HSD17B7P2):​n.742-1994G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0515 in 152,218 control chromosomes in the GnomAD database, including 255 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 0.051 (255 hom., cov: 32)
• Consequence: HSD17B7P2 ENST00000494540.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280
• Publications: 3 publications found

Genes affected

HSD17B7P2 (HGNC:):

HSD17B7P2 (HGNC:28120): (hydroxysteroid 17-beta dehydrogenase 7 pseudogene 2)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.069 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HSD17B7P2	NR_003086.1	n.725-1994G>A		intron_variant	Intron 5 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HSD17B7P2	ENST00000494540.6	n.742-1994G>A		intron_variant	Intron 5 of 7	1
HSD17B7P2	ENST00000471365.1	n.650-1165G>A		intron_variant	Intron 5 of 8	6
HSD17B7P2	ENST00000812332.1	n.697-1994G>A		intron_variant	Intron 5 of 7
HSD17B7P2	ENST00000812333.1	n.761-1994G>A		intron_variant	Intron 6 of 8

Frequencies

GnomAD3 genomes AF: 0.0514 AC: 7820 AN: 152100 Hom.: 253 Cov.: 32

Gnomad AFR AF: 0.0302

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.0447

Gnomad ASJ AF: 0.0544

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0562

Gnomad FIN AF: 0.0395

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0707

Gnomad OTH AF: 0.0526

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

GnomAD4 genome AF: 0.0515 AC: 7839 AN: 152218 Hom.: 255 Cov.: 32 AF XY: 0.0504 AC XY: 3748 AN XY: 74420

African (AFR) AF: 0.0304 AC: 1263 AN: 41536

American (AMR) AF: 0.0447 AC: 682 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0544 AC: 189 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5188

South Asian (SAS) AF: 0.0572 AC: 276 AN: 4822

European-Finnish (FIN) AF: 0.0395 AC: 418 AN: 10592

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0707 AC: 4809 AN: 68020

Other (OTH) AF: 0.0520 AC: 110 AN: 2114

Alfa AF: 0.0640 Hom.: 137

Bravo AF: 0.0516

Asia WGS AF: 0.0210 AC: 73 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.6
DANN	Benign	0.74
PhyloP100		-0.028

Splicing

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

Other links and lift over

dbSNP: rs2804672; hg19: chr10-38656887;