10-89432879-G-T

Position:

• chr10-89432879-G-T

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_Strong BP6_Very_Strong BS2

The NM_213606.4(SLC16A12):​c.*185C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.011 in 799,598 control chromosomes in the GnomAD database, including 76 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0097 (11 hom., cov: 32)
  • Exomes 𝑓: 0.011 (65 hom.)
• Consequence: SLC16A12 NM_213606.4 3_prime_UTR
• Clinical Significance: Likely benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 1.32

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]

ACMG classification

Verdict is Benign. Variant got -16 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BP6: Variant 10-89432879-G-T is Benign according to our data. Variant chr10-89432879-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 1190162.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS2: High AC in GnomAd4 at 1476 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC16A12	NM_213606.4	c.*185C>A		3_prime_UTR_variant	8/8	ENST00000371790.5	NP_998771.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC16A12	ENST00000371790.5	c.*185C>A		3_prime_UTR_variant	8/8	2	NM_213606.4	ENSP00000360855	P1

Frequencies

GnomAD3 genomes AF: 0.00971 AC: 1478 AN: 152158 Hom.: 11 Cov.: 32

Gnomad AFR AF: 0.00241

Gnomad AMI AF: 0.0396

Gnomad AMR AF: 0.00996

Gnomad ASJ AF: 0.0259

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00145

Gnomad FIN AF: 0.0109

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0140

Gnomad OTH AF: 0.00956

GnomAD4 exome AF: 0.0113 AC: 7335 AN: 647322 Hom.: 65 Cov.: 9 AF XY: 0.0112 AC XY: 3718 AN XY: 332486

Gnomad4 AFR exome AF: 0.00354

Gnomad4 AMR exome AF: 0.00870

Gnomad4 ASJ exome AF: 0.0234

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00191

Gnomad4 FIN exome AF: 0.0108

Gnomad4 NFE exome AF: 0.0130

Gnomad4 OTH exome AF: 0.0117

GnomAD4 genome AF: 0.00969 AC: 1476 AN: 152276 Hom.: 11 Cov.: 32 AF XY: 0.00955 AC XY: 711 AN XY: 74456

Gnomad4 AFR AF: 0.00245

Gnomad4 AMR AF: 0.00994

Gnomad4 ASJ AF: 0.0259

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00145

Gnomad4 FIN AF: 0.0109

Gnomad4 NFE AF: 0.0139

Gnomad4 OTH AF: 0.00946

Alfa AF: 0.00732 Hom.: 1

Bravo AF: 0.00957

Asia WGS AF: 0.00202 AC: 7 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 28, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.9
DANN	Benign	0.68

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

Other links and lift over

dbSNP: rs112629946; hg19: chr10-91192636;