rs1499793

Variant names:

• chr3-157643508-C-T
• rs1499793
• ENST00000461040.5:n.232-2260C>T

Variant summary

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

The ENST00000461040.5(SLC66A1LP):​n.232-2260C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,062 control chromosomes in the GnomAD database, including 4,088 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 0.22 (4088 hom., cov: 32)
• Consequence: SLC66A1LP ENST00000461040.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.399
• Publications: 4 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.312 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.232-2260C>T		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32955 AN: 151942 Hom.: 4083 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.217 AC: 32965 AN: 152062 Hom.: 4088 Cov.: 32 AF XY: 0.218 AC XY: 16229 AN XY: 74324

African (AFR) AF: 0.104 AC: 4317 AN: 41506

American (AMR) AF: 0.192 AC: 2924 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 693 AN: 3468

East Asian (EAS) AF: 0.325 AC: 1677 AN: 5162

South Asian (SAS) AF: 0.170 AC: 818 AN: 4822

European-Finnish (FIN) AF: 0.350 AC: 3700 AN: 10558

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.266 AC: 18058 AN: 67962

Other (OTH) AF: 0.246 AC: 521 AN: 2114

Alfa AF: 0.235 Hom.: 966

Bravo AF: 0.203

Asia WGS AF: 0.256 AC: 889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.9
DANN	Benign	0.72
PhyloP100		-0.40
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: rs1499793; hg19: chr3-157361297;