17-7037074-G-T

Variant names:

• chr17-7037074-G-T
• rs312457
• NM_201566.3:c.343+204G>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_201566.3(SLC16A13):​c.343+204G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000125 in 152,098 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.00012 (0 hom., cov: 31)
  • Exomes 𝑓: 0.000011 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SLC16A13 NM_201566.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05
• Publications: 41 publications found

Genes affected

SLC16A13 (HGNC:31037): (solute carrier family 16 member 13) Predicted to enable monocarboxylic acid transmembrane transporter activity. Predicted to be involved in monocarboxylic acid transport. Located in Golgi apparatus and cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_201566.3. 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
	SLC16A13	NM_201566.3	MANE Select	c.343+204G>T		intron	N/A	NP_963860.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC16A13	ENST00000308027.7	TSL:1 MANE Select	c.343+204G>T		intron	N/A	ENSP00000309751.6
	SLC16A13	ENST00000575844.1	TSL:6	n.*10G>T		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.000125 AC: 19 AN: 151980 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.000363

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000131

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.000957

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000108 AC: 5 AN: 463046 Hom.: 0 Cov.: 6 AF XY: 0.0000125 AC XY: 3 AN XY: 240228

African (AFR) AF: 0.0000824 AC: 1 AN: 12140

American (AMR) AF: 0.000143 AC: 2 AN: 14010

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12014

East Asian (EAS) AF: 0.00 AC: 0 AN: 25530

South Asian (SAS) AF: 0.00 AC: 0 AN: 42078

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 24232

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1842

European-Non Finnish (NFE) AF: 0.00000326 AC: 1 AN: 306806

Other (OTH) AF: 0.0000410 AC: 1 AN: 24394

GnomAD4 genome AF: 0.000125 AC: 19 AN: 152098 Hom.: 0 Cov.: 31 AF XY: 0.0000807 AC XY: 6 AN XY: 74366

African (AFR) AF: 0.000362 AC: 15 AN: 41454

American (AMR) AF: 0.000131 AC: 2 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5172

South Asian (SAS) AF: 0.00 AC: 0 AN: 4822

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10582

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 68000

Other (OTH) AF: 0.000947 AC: 2 AN: 2112

Alfa AF: 0.00 Hom.: 110607

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.43
PhyloP100		-2.0

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: rs312457; hg19: chr17-6940393;