rs9457841

Variant names:

• chr6-160129897-T-A
• rs9457841
• NM_003057.3:c.412-207T>A

Your query was ambiguous. Multiple possible variants found:

• chr6-160129897-T-A
• chr6-160129897-T-C
• chr6-160129897-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_003057.3(SLC22A1):​c.412-207T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SLC22A1 NM_003057.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91
• Publications: 6 publications found

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

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003057.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC22A1	NM_003057.3	MANE Select	c.412-207T>A		intron	N/A	NP_003048.1
	SLC22A1	NM_153187.2		c.412-207T>A		intron	N/A	NP_694857.1
	SLC22A1	NM_001437335.1		c.412-207T>A		intron	N/A	NP_001424264.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC22A1	ENST00000366963.9	TSL:1 MANE Select	c.412-207T>A		intron	N/A	ENSP00000355930.4
	SLC22A1	ENST00000540443.1	TSL:3	c.-372T>A		5_prime_UTR	Exon 1 of 3	ENSP00000440105.1
	SLC22A1	ENST00000898298.1		c.526-207T>A		intron	N/A	ENSP00000568357.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 395560 Hom.: 0 Cov.: 3 AF XY: 0.00 AC XY: 0 AN XY: 207776

African (AFR) AF: 0.00 AC: 0 AN: 11146

American (AMR) AF: 0.00 AC: 0 AN: 16422

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12166

East Asian (EAS) AF: 0.00 AC: 0 AN: 27550

South Asian (SAS) AF: 0.00 AC: 0 AN: 38690

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 26762

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1736

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 238228

Other (OTH) AF: 0.00 AC: 0 AN: 22860

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.57
DANN	Benign	0.31
PhyloP100		-1.9
PromoterAI		0.0022	Neutral

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs9457841; hg19: chr6-160550929;