rs1556611

Variant names:

• chr10-89443457-G-A
• rs1556611
• NM_213606.4:c.304+299C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-89443457-G-A
• chr10-89443457-G-T

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.761
• Publications: 2 publications found

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-AS1 (HGNC:51205): (SLC16A12 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_213606.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC16A12	NM_213606.4	MANE Select	c.304+299C>T		intron	N/A	NP_998771.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC16A12	ENST00000371790.5	TSL:2 MANE Select	c.304+299C>T		intron	N/A	ENSP00000360855.4
	SLC16A12-AS1	ENST00000765073.1		n.99+11243G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54450 AN: 151878 Hom.: 10078 Cov.: 32

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.: 32 AF XY: 0.355 AC XY: 26398 AN XY: 74316

African (AFR) AF: 0.435 AC: 18019 AN: 41462

American (AMR) AF: 0.252 AC: 3845 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1099 AN: 3464

East Asian (EAS) AF: 0.267 AC: 1381 AN: 5172

South Asian (SAS) AF: 0.358 AC: 1723 AN: 4818

European-Finnish (FIN) AF: 0.368 AC: 3886 AN: 10550

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.345 AC: 23418 AN: 67932

Other (OTH) AF: 0.349 AC: 737 AN: 2112

Alfa AF: 0.340 Hom.: 34607

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

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.58
DANN	Benign	0.41
PhyloP100		-0.76
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: rs1556611; hg19: chr10-91203214;