rs1353890

Variant names:

• chr3-157642608-T-C
• rs1353890
• ENST00000461040.5:n.232-3160T>C

Variant summary

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

The ENST00000461040.5(SLC66A1LP):​n.232-3160T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0376 in 152,272 control chromosomes in the GnomAD database, including 252 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 0.038 (252 hom., cov: 32)
• Consequence: SLC66A1LP ENST00000461040.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60
• Publications: 1 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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.178 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.232-3160T>C		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.0375 AC: 5704 AN: 152154 Hom.: 247 Cov.: 32

Gnomad AFR AF: 0.00702

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0957

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.0403

Gnomad FIN AF: 0.0587

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0292

Gnomad OTH AF: 0.0363

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

GnomAD4 genome AF: 0.0376 AC: 5719 AN: 152272 Hom.: 252 Cov.: 32 AF XY: 0.0411 AC XY: 3062 AN XY: 74438

African (AFR) AF: 0.00700 AC: 291 AN: 41568

American (AMR) AF: 0.0967 AC: 1478 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0239 AC: 83 AN: 3468

East Asian (EAS) AF: 0.188 AC: 971 AN: 5168

South Asian (SAS) AF: 0.0408 AC: 197 AN: 4830

European-Finnish (FIN) AF: 0.0587 AC: 623 AN: 10610

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0292 AC: 1987 AN: 68016

Other (OTH) AF: 0.0359 AC: 76 AN: 2116

Alfa AF: 0.0347 Hom.: 22

Bravo AF: 0.0400

Asia WGS AF: 0.110 AC: 382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.22
DANN	Benign	0.71
PhyloP100		-1.6
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: rs1353890; hg19: chr3-157360397;