rs1564348

chr6-160157828-T-C

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The NM_003057.3(SLC22A1):c.1599-688T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,208 control chromosomes in the GnomAD database, including 1,738 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).

• Frequency: Genomes: 𝑓 0.14 (1738 hom., cov: 32)
• Consequence: SLC22A1 NM_003057.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

Genes affected

SLC22A1 (HGNC:10963): (solute carrier family 22 member 1) Polyspecific organic cation transporters in the liver, kidney, intestine, and other organs are critical for elimination of many endogenous small organic cations as well as a wide array of drugs and environmental toxins. This gene is one of three similar cation transporter genes located in a cluster on chromosome 6. The encoded protein contains twelve putative transmembrane domains and is a plasma integral membrane protein. Two transcript variants encoding two different isoforms have been found for this gene, but only the longer variant encodes a functional transporter. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BP6: Variant 6-160157828-T-C is Benign according to our data. Variant chr6-160157828-T-C is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC22A1	NM_003057.3	c.1599-688T>C		intron_variant		ENST00000366963.9
SLC22A1	NM_153187.2	c.1486-688T>C		intron_variant
SLC22A1	XM_005267103.3	c.1687-688T>C		intron_variant
SLC22A1	XM_006715552.3	c.1386-688T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC22A1	ENST00000366963.9	c.1599-688T>C		intron_variant		1	NM_003057.3	P1

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21746 AN: 152090 Hom.: 1733 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.0986

Gnomad EAS AF: 0.00366

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.143 AC: 21768 AN: 152208 Hom.: 1738 Cov.: 32 AF XY: 0.144 AC XY: 10703 AN XY: 74416

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.208

Gnomad4 ASJ AF: 0.0986

Gnomad4 EAS AF: 0.00367

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.137

Alfa AF: 0.154 Hom.: 4453

Bravo AF: 0.146

Asia WGS AF: 0.0630 AC: 218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.42
Dann	Benign	0.58

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1564348; hg19: chr6-160578860;