rs995343

Variant names:

• chr12-59685594-G-A
• rs995343
• NM_001270623.2:c.-30-19178G>A

Your query was ambiguous. Multiple possible variants found:

• chr12-59685594-G-A
• chr12-59685594-G-C
• chr12-59685594-G-T

Variant summary

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

The NM_001270623.2(SLC16A7):​c.-30-19178G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.566 in 151,890 control chromosomes in the GnomAD database, including 25,321 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 0.57 (25321 hom., cov: 32)
• Consequence: SLC16A7 NM_001270623.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.352
• Publications: 6 publications found

Genes affected

SLC16A7 (HGNC:10928): (solute carrier family 16 member 7) This gene is a member of the monocarboxylate transporter family. Members in this family transport metabolites, such as lactate, pyruvate, and ketone bodies. The protein encoded by this gene catalyzes the proton-linked transport of monocarboxylates and has the highest affinity for pyruvate. This protein has been reported to be more highly expressed in prostate and colorectal cancer specimens when compared to control specimens. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2012]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001270623.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC16A7	NM_001270623.2	MANE Select	c.-30-19178G>A		intron	N/A	NP_001257552.1	O60669
	SLC16A7	NM_001270622.2		c.-10-19198G>A		intron	N/A	NP_001257551.1	O60669

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC16A7	ENST00000547379.6	TSL:1 MANE Select	c.-30-19178G>A		intron	N/A	ENSP00000448071.1	O60669
	SLC16A7	ENST00000552432.5	TSL:1	c.-10-19198G>A		intron	N/A	ENSP00000449547.1	O60669
	SLC16A7	ENST00000858943.1		c.-30-19178G>A		intron	N/A	ENSP00000529002.1

Frequencies

GnomAD3 genomes AF: 0.566 AC: 85954 AN: 151770 Hom.: 25284 Cov.: 32

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.594

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.566 AC: 86042 AN: 151890 Hom.: 25321 Cov.: 32 AF XY: 0.564 AC XY: 41833 AN XY: 74210

African (AFR) AF: 0.734 AC: 30423 AN: 41472

American (AMR) AF: 0.474 AC: 7237 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.496 AC: 1720 AN: 3466

East Asian (EAS) AF: 0.326 AC: 1675 AN: 5138

South Asian (SAS) AF: 0.511 AC: 2461 AN: 4816

European-Finnish (FIN) AF: 0.520 AC: 5467 AN: 10510

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.519 AC: 35259 AN: 67904

Other (OTH) AF: 0.536 AC: 1131 AN: 2112

Alfa AF: 0.525 Hom.: 13848

Bravo AF: 0.566

Asia WGS AF: 0.427 AC: 1483 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.53
DANN	Benign	0.59
PhyloP100		-0.35
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: rs995343; hg19: chr12-60079375;