rs8190478

Positions:

• chr9-96302601-G-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.2561-290C>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 0.265 in 152,044 control chromosomes in the GnomAD database, including 6,285 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 0.26 (6285 hom., cov: 32)
• Consequence: SLC35D2-HSD17B3 NR_182427.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460

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 (NFE) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC35D2-HSD17B3	NR_182427.1	n.2561-290C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000464104.6	n.264-290C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40222 AN: 151924 Hom.: 6289 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.265 AC: 40226 AN: 152044 Hom.: 6285 Cov.: 32 AF XY: 0.257 AC XY: 19137 AN XY: 74344

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.233

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.327

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.272

Alfa AF: 0.314 Hom.: 2898

Bravo AF: 0.253

Asia WGS AF: 0.221 AC: 766 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.99
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8190478; hg19: chr9-99064883;