rs10435946

chr9-84340893-C-Achr9-84340893-C-G

Variant summary

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

The ENST00000650453.1(ENSG00000285987):n.536+23844C>A 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 0.228 in 151,830 control chromosomes in the GnomAD database, including 5,282 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 0.23 (5282 hom., cov: 30)
• Consequence: ENST00000650453.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.592

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC28A3	NM_022127.3	c.-45-215G>T		intron_variant
SLC28A3	XM_011518906.3	c.-45-215G>T		intron_variant
SLC28A3	XM_011518907.3	c.-97-27439G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000650453.1	n.536+23844C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34519 AN: 151712 Hom.: 5274 Cov.: 30

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.0352

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.228 AC: 34561 AN: 151830 Hom.: 5282 Cov.: 30 AF XY: 0.227 AC XY: 16816 AN XY: 74186

Gnomad4 AFR AF: 0.426

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.184

Alfa AF: 0.180 Hom.: 1541

Bravo AF: 0.232

Asia WGS AF: 0.255 AC: 889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	2.3
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10435946; hg19: chr9-86955808;