chr6-160148750-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NM_003057.3(SLC22A1):​c.1385+5101T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0122 in 151,756 control chromosomes in the GnomAD database, including 33 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 0.012 ( 33 hom., cov: 30)

Consequence

SLC22A1
NM_003057.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.69
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0122 (1851/151756) while in subpopulation AFR AF= 0.0422 (1745/41354). AF 95% confidence interval is 0.0405. There are 33 homozygotes in gnomad4. There are 882 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 33 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SLC22A1NM_003057.3 linkuse as main transcriptc.1385+5101T>G intron_variant ENST00000366963.9 NP_003048.1
SLC22A1NM_153187.2 linkuse as main transcriptc.1385+5101T>G intron_variant NP_694857.1
SLC22A1XM_005267103.3 linkuse as main transcriptc.1385+5101T>G intron_variant XP_005267160.1
SLC22A1XM_006715552.3 linkuse as main transcriptc.1385+5101T>G intron_variant XP_006715615.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SLC22A1ENST00000366963.9 linkuse as main transcriptc.1385+5101T>G intron_variant 1 NM_003057.3 ENSP00000355930 P1O15245-1

Frequencies

GnomAD3 genomes
AF:
0.0122
AC:
1849
AN:
151640
Hom.:
33
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.0423
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00499
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000208
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.000133
Gnomad OTH
AF:
0.00909
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0122
AC:
1851
AN:
151756
Hom.:
33
Cov.:
30
AF XY:
0.0119
AC XY:
882
AN XY:
74156
show subpopulations
Gnomad4 AFR
AF:
0.0422
Gnomad4 AMR
AF:
0.00498
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000208
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000133
Gnomad4 OTH
AF:
0.00900

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
0.16
DANN
Benign
0.57

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7750592; hg19: chr6-160569782; API