rs2830

Variant names:

• chr17-42552545-G-A
• rs2830
• ENST00000590513.3:n.2297C>T

Your query was ambiguous. Multiple possible variants found:

• chr17-42552545-G-A
• chr17-42552545-G-T

Variant summary

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

The NR_144402.1(HSD17B1-AS1):​n.2258C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 239,470 control chromosomes in the GnomAD database, including 37,952 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 0.57 (25517 hom., cov: 32)
  • Exomes 𝑓: 0.52 (12435 hom.)
• Consequence: HSD17B1-AS1 NR_144402.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.257
• Publications: 33 publications found

Genes affected

HSD17B1-AS1 (HGNC:55314): (HSD17B1 antisense RNA 1)

ENSG00000266929 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_144402.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HSD17B1-AS1	NR_144402.1		n.2258C>T		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HSD17B1-AS1	ENST00000590513.3	TSL:6	n.2297C>T		non_coding_transcript_exon	Exon 1 of 1
	HSD17B1-AS1	ENST00000803215.1		n.1283C>T		non_coding_transcript_exon	Exon 2 of 2
	HSD17B1-AS1	ENST00000803216.1		n.1223C>T		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.574 AC: 87198 AN: 151868 Hom.: 25487 Cov.: 32

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.522

GnomAD4 exome AF: 0.522 AC: 45705 AN: 87484 Hom.: 12435 Cov.: 0 AF XY: 0.525 AC XY: 23922 AN XY: 45582

African (AFR) AF: 0.645 AC: 1555 AN: 2410

American (AMR) AF: 0.516 AC: 2241 AN: 4342

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 887 AN: 2554

East Asian (EAS) AF: 0.402 AC: 1809 AN: 4500

South Asian (SAS) AF: 0.594 AC: 6553 AN: 11024

European-Finnish (FIN) AF: 0.493 AC: 1850 AN: 3750

Middle Eastern (MID) AF: 0.372 AC: 128 AN: 344

European-Non Finnish (NFE) AF: 0.527 AC: 28284 AN: 53710

Other (OTH) AF: 0.494 AC: 2398 AN: 4850

GnomAD4 genome AF: 0.574 AC: 87284 AN: 151986 Hom.: 25517 Cov.: 32 AF XY: 0.570 AC XY: 42371 AN XY: 74302

African (AFR) AF: 0.683 AC: 28295 AN: 41448

American (AMR) AF: 0.502 AC: 7663 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 1353 AN: 3464

East Asian (EAS) AF: 0.438 AC: 2264 AN: 5168

South Asian (SAS) AF: 0.640 AC: 3087 AN: 4824

European-Finnish (FIN) AF: 0.530 AC: 5593 AN: 10558

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.550 AC: 37371 AN: 67940

Other (OTH) AF: 0.526 AC: 1109 AN: 2110

Alfa AF: 0.563 Hom.: 3140

Bravo AF: 0.573

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.0
DANN	Benign	0.43
PhyloP100		-0.26
PromoterAI		0.012	Neutral
Mutation Taster		=300/0	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: rs2830; hg19: chr17-40704563;