rs9849733

Variant names:

• chr3-157676472-T-C
• rs9849733
• ENST00000461040.5:n.339-1053T>C

Variant summary

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

The ENST00000461040.5(SLC66A1LP):​n.339-1053T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 152,092 control chromosomes in the GnomAD database, including 17,089 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 0.38 (17089 hom., cov: 32)
• Consequence: SLC66A1LP ENST00000461040.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510
• Publications: 3 publications found

Genes affected

SLC66A1LP (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC66A1LP	ENST00000461040.5	n.339-1053T>C		intron_variant	Intron 3 of 3	3

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58332 AN: 151972 Hom.: 17033 Cov.: 32

Gnomad AFR AF: 0.829

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.384 AC: 58447 AN: 152092 Hom.: 17089 Cov.: 32 AF XY: 0.379 AC XY: 28191 AN XY: 74348

African (AFR) AF: 0.830 AC: 34429 AN: 41492

American (AMR) AF: 0.250 AC: 3821 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 620 AN: 3466

East Asian (EAS) AF: 0.293 AC: 1518 AN: 5174

South Asian (SAS) AF: 0.152 AC: 733 AN: 4822

European-Finnish (FIN) AF: 0.269 AC: 2841 AN: 10574

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13585 AN: 67988

Other (OTH) AF: 0.363 AC: 767 AN: 2112

Alfa AF: 0.295 Hom.: 1769

Bravo AF: 0.406

Asia WGS AF: 0.291 AC: 1009 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.5
DANN	Benign	0.79
PhyloP100		-0.051
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs9849733; hg19: chr3-157394261;