Variant chr3-38306515-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001320033.2(SLC22A14):c.489C>T(p.Asp163Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0064 in 1,613,722 control chromosomes in the GnomAD database, including 39 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0041 ( 2 hom., cov: 33)

Exomes 𝑓: 0.0066 ( 37 hom. )

Consequence

SLC22A14
NM_001320033.2 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.21

Variant links:

Genes affected

SLC22A14 (HGNC:8495): (solute carrier family 22 member 14) This gene encodes a member of the organic-cation transporter family. It is located in a gene cluster with another member of the family, organic cation transporter like 3. The encoded protein is a transmembrane protein which is thought to transport small molecules and since this protein is conserved among several species, it is suggested to have a fundamental role in mammalian systems. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]

SLC22A14 links:

SLC22A14 (HGNC:):

SLC22A14 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BP6

Variant 3-38306515-C-T is Benign according to our data. Variant chr3-38306515-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2653670.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-2.21 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC22A14	NM_001320033.2 linkuse as main transcript	c.489C>T	p.Asp163Asp	synonymous_variant	2/11	ENST00000448498.6	NP_001306962.1	Q9Y267

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
SLC22A14	ENST00000448498.6 linkuse as main transcript	c.489C>T	p.Asp163Asp	synonymous_variant	2/11	1	NM_001320033.2	ENSP00000396283.1	Q9Y267
SLC22A14	ENST00000273173.4 linkuse as main transcript	c.489C>T	p.Asp163Asp	synonymous_variant	1/10	1		ENSP00000273173.4	Q9Y267
SLC22A14	ENST00000466887.5 linkuse as main transcript	c.93C>T	p.Asp31Asp	synonymous_variant	2/4	4		ENSP00000442528.1	F5H7H1
SLC22A14	ENST00000496724.1 linkuse as main transcript	n.1342C>T		non_coding_transcript_exon_variant	1/2	2

Frequencies

GnomAD3 genomes

AF:

0.00408

AC:

621

AN:

152190

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00113

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00373

Gnomad ASJ

AF:

0.000577

Gnomad EAS

AF:

0.000577

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00113

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00723

Gnomad OTH

AF:

0.00287

GnomAD3 exomes

AF:

0.00356

AC:

889

AN:

249632

Hom.:

AF XY:

0.00339

AC XY:

457

AN XY:

134990

show subpopulations

Gnomad AFR exome

AF:

0.00105

Gnomad AMR exome

AF:

0.00191

Gnomad ASJ exome

AF:

0.000200

Gnomad EAS exome

AF:

0.000761

Gnomad SAS exome

AF:

0.000196

Gnomad FIN exome

AF:

0.000972

Gnomad NFE exome

AF:

0.00649

Gnomad OTH exome

AF:

0.00572

GnomAD4 exome

AF:

0.00664

AC:

9709

AN:

1461412

Hom.:

Cov.:

AF XY:

0.00639

AC XY:

4643

AN XY:

726986

show subpopulations

Gnomad4 AFR exome

AF:

0.00128

Gnomad4 AMR exome

AF:

0.00221

Gnomad4 ASJ exome

AF:

0.000230

Gnomad4 EAS exome

AF:

0.000302

Gnomad4 SAS exome

AF:

0.000232

Gnomad4 FIN exome

AF:

0.00110

Gnomad4 NFE exome

AF:

0.00814

Gnomad4 OTH exome

AF:

0.00676

GnomAD4 genome

AF:

0.00407

AC:

620

AN:

152310

Hom.:

Cov.:

AF XY:

0.00376

AC XY:

280

AN XY:

74480

show subpopulations

Gnomad4 AFR

AF:

0.00113

Gnomad4 AMR

AF:

0.00372

Gnomad4 ASJ

AF:

0.000577

Gnomad4 EAS

AF:

0.000578

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00113

Gnomad4 NFE

AF:

0.00722

Gnomad4 OTH

AF:

0.00284

Alfa

AF:

0.00545

Hom.:

Bravo

AF:

0.00439

Asia WGS

AF:

0.000289

AC:

AN:

3478

EpiCase

AF:

0.00671

EpiControl

AF:

0.00599

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jul 01, 2022

SLC22A14: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

1.1

DANN

Benign

0.62

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over