rs8190480

Variant names:

• chr9-96302506-T-A
• rs8190480
• ENST00000643789.1:n.*1470-195A>T

Variant summary

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

The ENST00000643789.1(ENSG00000285269):​n.*1470-195A>T variant causes a intron 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: ENSG00000285269 ENST00000643789.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.416
• Publications: 0 publications found

Genes affected

ENSG00000285269 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLC35D2-HSD17B3	NR_182427.1	n.2561-195A>T		intron_variant	Intron 15 of 25

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285269	ENST00000643789.1	n.*1470-195A>T		intron_variant	Intron 11 of 21			ENSP00000494818.1
ENSG00000285269	ENST00000463517.2	n.603-195A>T		intron_variant	Intron 3 of 15	5
ENSG00000285269	ENST00000464104.6	n.264-195A>T		intron_variant	Intron 2 of 15	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

African (AFR) AF: 0.0303 AC: 1259 AN: 41562

American (AMR) AF: 0.00987 AC: 151 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.00490 AC: 17 AN: 3472

East Asian (EAS) AF: 0.0563 AC: 292 AN: 5190

South Asian (SAS) AF: 0.0642 AC: 310 AN: 4826

European-Finnish (FIN) AF: 0.00461 AC: 49 AN: 10622

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.00712 AC: 484 AN: 68022

Other (OTH) AF: 0.0194 AC: 41 AN: 2112

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
PhyloP100		-0.42
PromoterAI		-0.0066	Neutral

Splicing

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

Other links and lift over

dbSNP: rs8190480; hg19: chr9-99064788;