1-19331678-C-T

Variant names:

• chr1-19331678-C-T
• rs12117357
• NR_109848.2:n.1889C>T

Variant summary

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

The NR_109848.2(SLC66A1):​n.1889C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 152,142 control chromosomes in the GnomAD database, including 3,044 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 0.19 (3044 hom., cov: 33)
• Consequence: SLC66A1 NR_109848.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.656
• Publications: 10 publications found

Genes affected

SLC66A1 (HGNC:26001): (solute carrier family 66 member 1) Enables L-arginine transmembrane transporter activity and L-lysine transmembrane transporter activity. Involved in L-arginine transmembrane transport; amino acid homeostasis; and lysine transport. Located in lysosomal membrane. Is integral component of organelle membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_109848.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC66A1	NR_109848.2		n.1889C>T		non_coding_transcript_exon	Exon 10 of 10

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28532 AN: 152022 Hom.: 3047 Cov.: 33

Gnomad AFR AF: 0.0843

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.188 AC: 28532 AN: 152142 Hom.: 3044 Cov.: 33 AF XY: 0.192 AC XY: 14307 AN XY: 74356

African (AFR) AF: 0.0843 AC: 3502 AN: 41556

American (AMR) AF: 0.218 AC: 3325 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 719 AN: 3472

East Asian (EAS) AF: 0.204 AC: 1055 AN: 5162

South Asian (SAS) AF: 0.211 AC: 1018 AN: 4824

European-Finnish (FIN) AF: 0.292 AC: 3090 AN: 10568

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.223 AC: 15171 AN: 67974

Other (OTH) AF: 0.181 AC: 384 AN: 2116

Alfa AF: 0.207 Hom.: 473

Bravo AF: 0.179

Asia WGS AF: 0.190 AC: 657 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.8
DANN	Benign	0.34
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs12117357; hg19: chr1-19658172; COSMIC: COSV64320747;