rs10784000

Positions:

• chr12-59787183-G-A
• chr12-59787183-G-C
• chr12-59787183-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001270623.2(SLC16A7):​c.*7504G>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 0.723 in 151,912 control chromosomes in the GnomAD database, including 40,149 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 0.72 (40149 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: SLC16A7 NM_001270623.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.215

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC16A7	NM_001270623.2	c.*7504G>A		3_prime_UTR_variant	6/6	ENST00000547379.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC16A7	ENST00000547379.6	c.*7504G>A		3_prime_UTR_variant	6/6	1	NM_001270623.2	P1
SLC16A7	ENST00000261187.8	c.*7504G>A		3_prime_UTR_variant	5/5	1		P1

Frequencies

GnomAD3 genomes AF: 0.722 AC: 109658 AN: 151792 Hom.: 40108 Cov.: 31

Gnomad AFR AF: 0.849

Gnomad AMI AF: 0.700

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.678

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.696

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.723 AC: 109760 AN: 151912 Hom.: 40149 Cov.: 31 AF XY: 0.722 AC XY: 53585 AN XY: 74258

Gnomad4 AFR AF: 0.849

Gnomad4 AMR AF: 0.667

Gnomad4 ASJ AF: 0.676

Gnomad4 EAS AF: 0.733

Gnomad4 SAS AF: 0.675

Gnomad4 FIN AF: 0.681

Gnomad4 NFE AF: 0.670

Gnomad4 OTH AF: 0.696

Alfa AF: 0.681 Hom.: 18555

Bravo AF: 0.727

Asia WGS AF: 0.669 AC: 2316 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.50
DANN	Benign	0.54

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10784000; hg19: chr12-60180964;