dbSNP rs1556611: SLC16A12:c.304+299C>T (chr10-89443457-G-A) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_213606.4(SLC16A12):c.304+299C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 151,996 control chromosomes in the GnomAD database, including 10,093 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.36 ( 10093 hom., cov: 32)

Consequence

SLC16A12
NM_213606.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.761

Variant links:

Genes affected

SLC16A12 (HGNC:23094): (solute carrier family 16 member 12) This gene encodes a transmembrane transporter that likely plays a role in monocarboxylic acid transport. A mutation in this gene has been associated with juvenile cataracts with microcornea and renal glucosuria. [provided by RefSeq, Mar 2010]

SLC16A12 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 10-89443457-G-A is Benign according to our data. Variant chr10-89443457-G-A is described in ClinVar as [Benign]. Clinvar id is 1274623.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC16A12	NM_213606.4 link	c.304+299C>T		intron_variant	Intron 4 of 7	ENST00000371790.5	NP_998771.3	Q6ZSM3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC16A12	ENST00000371790.5 link	c.304+299C>T		intron_variant	Intron 4 of 7	2	NM_213606.4	ENSP00000360855.4		Q6ZSM3

Frequencies

GnomAD3 genomes

AF:

0.359

AC:

54450

AN:

151878

Hom.:

10078

Cov.:

show subpopulations

Gnomad AFR

AF:

0.434

Gnomad AMI

AF:

0.325

Gnomad AMR

AF:

0.252

Gnomad ASJ

AF:

0.317

Gnomad EAS

AF:

0.268

Gnomad SAS

AF:

0.360

Gnomad FIN

AF:

0.368

Gnomad MID

AF:

0.335

Gnomad NFE

AF:

0.345

Gnomad OTH

AF:

0.346

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.359

AC:

54503

AN:

151996

Hom.:

10093

Cov.:

AF XY:

0.355

AC XY:

26398

AN XY:

74316

show subpopulations

Gnomad4 AFR

AF:

0.435

Gnomad4 AMR

AF:

0.252

Gnomad4 ASJ

AF:

0.317

Gnomad4 EAS

AF:

0.267

Gnomad4 SAS

AF:

0.358

Gnomad4 FIN

AF:

0.368

Gnomad4 NFE

AF:

0.345

Gnomad4 OTH

AF:

0.349

Alfa

AF:

0.333

Hom.:

14348

Bravo

AF:

0.350

Asia WGS

AF:

0.372

AC:

1291

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Jun 29, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.58

DANN

Benign

0.41

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