rs4149178

Variant names:

• chr6-43304450-A-G
• rs4149178
• ENST00000372574.7:c.*172A>G

Variant summary

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

The ENST00000372574.7(SLC22A7):​c.*172A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 588,666 control chromosomes in the GnomAD database, including 10,622 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 0.21 (4063 hom., cov: 33)
  • Exomes 𝑓: 0.16 (6559 hom.)
• Consequence: SLC22A7 ENST00000372574.7 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0660
• Publications: 40 publications found

Genes affected

SLC22A7 (HGNC:10971): (solute carrier family 22 member 7) The protein encoded by this gene is involved in the sodium-independent transport and excretion of organic anions, some of which are potentially toxic. The encoded protein is an integral membrane protein and appears to be localized to the basolateral membrane of the kidney. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]

CRIP3 (HGNC:17751): (cysteine rich protein 3) Predicted to enable metal ion binding activity. Predicted to act upstream of or within T cell proliferation. Predicted to be located in cytoplasm. [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 (AFR) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000372574.7. 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
	SLC22A7	NM_153320.2	MANE Select	c.1592+206A>G		intron	N/A	NP_696961.2	Q9Y694-1
	SLC22A7	NM_006672.3		c.1586+206A>G		intron	N/A	NP_006663.2	Q9Y694-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC22A7	ENST00000372574.7	TSL:1	c.*172A>G		3_prime_UTR	Exon 9 of 9	ENSP00000361655.3	Q9Y694-3
	SLC22A7	ENST00000372585.10	TSL:5 MANE Select	c.1592+206A>G		intron	N/A	ENSP00000361666.5	Q9Y694-1
	SLC22A7	ENST00000875179.1		c.1745+206A>G		intron	N/A	ENSP00000545238.1

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32192 AN: 152014 Hom.: 4052 Cov.: 33

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.0477

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.229

GnomAD4 exome AF: 0.163 AC: 71268 AN: 436534 Hom.: 6559 Cov.: 5 AF XY: 0.163 AC XY: 37235 AN XY: 227908

African (AFR) AF: 0.345 AC: 3961 AN: 11494

American (AMR) AF: 0.228 AC: 3232 AN: 14164

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 2688 AN: 12938

East Asian (EAS) AF: 0.0556 AC: 1556 AN: 27992

South Asian (SAS) AF: 0.168 AC: 6402 AN: 38182

European-Finnish (FIN) AF: 0.149 AC: 4751 AN: 31792

Middle Eastern (MID) AF: 0.242 AC: 854 AN: 3526

European-Non Finnish (NFE) AF: 0.159 AC: 43255 AN: 271438

Other (OTH) AF: 0.183 AC: 4569 AN: 25008

GnomAD4 genome AF: 0.212 AC: 32247 AN: 152132 Hom.: 4063 Cov.: 33 AF XY: 0.208 AC XY: 15461 AN XY: 74388

African (AFR) AF: 0.347 AC: 14374 AN: 41430

American (AMR) AF: 0.207 AC: 3158 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 781 AN: 3472

East Asian (EAS) AF: 0.0480 AC: 249 AN: 5186

South Asian (SAS) AF: 0.156 AC: 754 AN: 4830

European-Finnish (FIN) AF: 0.136 AC: 1442 AN: 10614

Middle Eastern (MID) AF: 0.250 AC: 73 AN: 292

European-Non Finnish (NFE) AF: 0.159 AC: 10824 AN: 67990

Other (OTH) AF: 0.228 AC: 482 AN: 2114

Alfa AF: 0.178 Hom.: 5111

Bravo AF: 0.224

Asia WGS AF: 0.122 AC: 423 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	1.5
DANN	Benign	0.38
PhyloP100		0.066
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

Other links and lift over

dbSNP: rs4149178; hg19: chr6-43272188; COSMIC: COSV51486814; COSMIC: COSV51486814;