rs8190480

chr9-96302506-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_182427.1(SLC35D2-HSD17B3):n.2561-195A>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0172 in 152,314 control chromosomes in the GnomAD database, including 60 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 0.017 (60 hom., cov: 32)
• Consequence: SLC35D2-HSD17B3 NR_182427.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.416

Genes affected

SLC35D2-HSD17B3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0584 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC35D2-HSD17B3	NR_182427.1	n.2561-195A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000464104.6	n.264-195A>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0171 AC: 2608 AN: 152196 Hom.: 57 Cov.: 32

Gnomad AFR AF: 0.0301

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.00988

Gnomad ASJ AF: 0.00490

Gnomad EAS AF: 0.0563

Gnomad SAS AF: 0.0648

Gnomad FIN AF: 0.00461

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00711

Gnomad OTH AF: 0.0158

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

GnomAD4 genome AF: 0.0172 AC: 2625 AN: 152314 Hom.: 60 Cov.: 32 AF XY: 0.0179 AC XY: 1332 AN XY: 74486

Gnomad4 AFR AF: 0.0303

Gnomad4 AMR AF: 0.00987

Gnomad4 ASJ AF: 0.00490

Gnomad4 EAS AF: 0.0563

Gnomad4 SAS AF: 0.0642

Gnomad4 FIN AF: 0.00461

Gnomad4 NFE AF: 0.00712

Gnomad4 OTH AF: 0.0194

Alfa AF: 0.0105 Hom.: 0

Bravo AF: 0.0176

Asia WGS AF: 0.0690 AC: 238 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	0.53
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8190480; hg19: chr9-99064788;