rs312457

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr17-7037074-G-A
• chr17-7037074-G-C
• chr17-7037074-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_201566.3(SLC16A13):​c.343+204G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.968 in 614,950 control chromosomes in the GnomAD database, including 289,191 homozygotes. 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 0.94 (67806 hom., cov: 31)
  • Exomes 𝑓: 0.98 (221385 hom.)
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.986 is higher than 0.05.

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>A		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>A		intron	N/A	ENSP00000309751.6
	SLC16A13	ENST00000575844.1	TSL:6	n.*10G>A		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.942 AC: 143121 AN: 151912 Hom.: 67766 Cov.: 31

Gnomad AFR AF: 0.883

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.834

Gnomad ASJ AF: 0.991

Gnomad EAS AF: 0.903

Gnomad SAS AF: 0.991

Gnomad FIN AF: 0.979

Gnomad MID AF: 0.991

Gnomad NFE AF: 0.992

Gnomad OTH AF: 0.948

GnomAD4 exome AF: 0.977 AC: 452159 AN: 462918 Hom.: 221385 Cov.: 6 AF XY: 0.978 AC XY: 234993 AN XY: 240164

African (AFR) AF: 0.881 AC: 10678 AN: 12124

American (AMR) AF: 0.769 AC: 10747 AN: 13980

Ashkenazi Jewish (ASJ) AF: 0.988 AC: 11873 AN: 12012

East Asian (EAS) AF: 0.911 AC: 23250 AN: 25508

South Asian (SAS) AF: 0.996 AC: 41887 AN: 42074

European-Finnish (FIN) AF: 0.983 AC: 23810 AN: 24226

Middle Eastern (MID) AF: 0.992 AC: 1827 AN: 1842

European-Non Finnish (NFE) AF: 0.992 AC: 304436 AN: 306768

Other (OTH) AF: 0.970 AC: 23651 AN: 24384

GnomAD4 genome AF: 0.942 AC: 143219 AN: 152032 Hom.: 67806 Cov.: 31 AF XY: 0.941 AC XY: 69923 AN XY: 74328

African (AFR) AF: 0.883 AC: 36572 AN: 41416

American (AMR) AF: 0.834 AC: 12730 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.991 AC: 3440 AN: 3470

East Asian (EAS) AF: 0.903 AC: 4668 AN: 5170

South Asian (SAS) AF: 0.991 AC: 4778 AN: 4820

European-Finnish (FIN) AF: 0.979 AC: 10358 AN: 10580

Middle Eastern (MID) AF: 0.990 AC: 291 AN: 294

European-Non Finnish (NFE) AF: 0.992 AC: 67465 AN: 67994

Other (OTH) AF: 0.949 AC: 2005 AN: 2112

Alfa AF: 0.971 Hom.: 110607

Bravo AF: 0.923

Asia WGS AF: 0.944 AC: 3285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.50
DANN	Benign	0.78
PhyloP100		-2.0
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: rs312457; hg19: chr17-6940393;