rs4709400

Variant names:

• chr6-160122578-C-G
• rs4709400
• NM_003057.3:c.411+232C>G

Your query was ambiguous. Multiple possible variants found:

• chr6-160122578-C-G
• chr6-160122578-C-A
• chr6-160122578-C-T

Variant summary

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

The NM_003057.3(SLC22A1):​c.411+232C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 603,936 control chromosomes in the GnomAD database, including 17,801 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as (no stars).

• Frequency:
  • Genomes: 𝑓 0.29 (7021 hom., cov: 32)
  • Exomes 𝑓: 0.21 (10780 hom.)
• Consequence: SLC22A1 NM_003057.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.73
• Publications: 9 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

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.411+232C>G		intron	N/A	NP_003048.1	O15245-1
	SLC22A1	NM_153187.2		c.411+232C>G		intron	N/A	NP_694857.1	O15245-2
	SLC22A1	NM_001437335.1		c.411+232C>G		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.411+232C>G		intron	N/A	ENSP00000355930.4	O15245-1
	SLC22A1	ENST00000898298.1		c.411+232C>G		intron	N/A	ENSP00000568357.1
	SLC22A1	ENST00000898304.1		c.411+232C>G		intron	N/A	ENSP00000568363.1

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44172 AN: 151774 Hom.: 7001 Cov.: 32

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.271

GnomAD4 exome AF: 0.211 AC: 95216 AN: 452044 Hom.: 10780 AF XY: 0.211 AC XY: 44824 AN XY: 212730

African (AFR) AF: 0.391 AC: 3160 AN: 8074

American (AMR) AF: 0.307 AC: 151 AN: 492

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 347 AN: 2770

East Asian (EAS) AF: 0.505 AC: 941 AN: 1864

South Asian (SAS) AF: 0.261 AC: 2316 AN: 8874

European-Finnish (FIN) AF: 0.173 AC: 26 AN: 150

Middle Eastern (MID) AF: 0.186 AC: 170 AN: 916

European-Non Finnish (NFE) AF: 0.205 AC: 84759 AN: 414242

Other (OTH) AF: 0.228 AC: 3346 AN: 14662

GnomAD4 genome AF: 0.291 AC: 44245 AN: 151892 Hom.: 7021 Cov.: 32 AF XY: 0.292 AC XY: 21702 AN XY: 74220

African (AFR) AF: 0.400 AC: 16562 AN: 41374

American (AMR) AF: 0.315 AC: 4808 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 478 AN: 3470

East Asian (EAS) AF: 0.517 AC: 2658 AN: 5138

South Asian (SAS) AF: 0.273 AC: 1315 AN: 4810

European-Finnish (FIN) AF: 0.222 AC: 2345 AN: 10554

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15320 AN: 67960

Other (OTH) AF: 0.273 AC: 575 AN: 2108

Alfa AF: 0.121 Hom.: 188

Bravo AF: 0.307

Asia WGS AF: 0.405 AC: 1409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.072
DANN	Benign	0.30
PhyloP100		-2.7
Mutation Taster		=100/0	polymorphism (auto)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4709400;

hg19: chr6-160543610;