rs17087148

chr9-84354137-A-G

Variant summary

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

The ENST00000650453.1(ENSG00000285987):n.536+37088A>G 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 0.108 in 152,192 control chromosomes in the GnomAD database, including 1,531 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 0.11 (1531 hom., cov: 33)
• Consequence: ENST00000650453.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0210

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC28A3	NM_022127.3	c.-45-13459T>C		intron_variant
SLC28A3	XM_011518906.3	c.-45-13459T>C		intron_variant
SLC28A3	XM_011518907.3	c.-98+14315T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000650453.1	n.536+37088A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16350 AN: 152074 Hom.: 1517 Cov.: 33

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.0351

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.0908

Gnomad FIN AF: 0.0630

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0344

Gnomad OTH AF: 0.0922

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

GnomAD4 genome AF: 0.108 AC: 16416 AN: 152192 Hom.: 1531 Cov.: 33 AF XY: 0.109 AC XY: 8134 AN XY: 74410

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.0351

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.0919

Gnomad4 FIN AF: 0.0630

Gnomad4 NFE AF: 0.0344

Gnomad4 OTH AF: 0.0978

Alfa AF: 0.0532 Hom.: 470

Bravo AF: 0.123

Asia WGS AF: 0.207 AC: 718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	8.7
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17087148; hg19: chr9-86969052;