rs10784000

Variant names:

• chr12-59787183-G-A
• rs10784000
• NM_001270623.2:c.*7504G>A

Your query was ambiguous. Multiple possible variants found:

• chr12-59787183-G-A
• chr12-59787183-G-C
• chr12-59787183-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.*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
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.842 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC16A7	NM_001270623.2	MANE Select	c.*7504G>A		3_prime_UTR	Exon 6 of 6	NP_001257552.1
	SLC16A7	NR_073055.2		n.9348G>A		non_coding_transcript_exon	Exon 7 of 7
	SLC16A7	NR_073056.2		n.9209G>A		non_coding_transcript_exon	Exon 7 of 7

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC16A7	ENST00000547379.6	TSL:1 MANE Select	c.*7504G>A		3_prime_UTR	Exon 6 of 6	ENSP00000448071.1
	SLC16A7	ENST00000261187.8	TSL:1	c.*7504G>A		3_prime_UTR	Exon 5 of 5	ENSP00000261187.4

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.849 AC: 35224 AN: 41488

American (AMR) AF: 0.667 AC: 10168 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.676 AC: 2347 AN: 3470

East Asian (EAS) AF: 0.733 AC: 3796 AN: 5176

South Asian (SAS) AF: 0.675 AC: 3255 AN: 4820

European-Finnish (FIN) AF: 0.681 AC: 7167 AN: 10518

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.670 AC: 45505 AN: 67880

Other (OTH) AF: 0.696 AC: 1464 AN: 2104

Alfa AF: 0.682 Hom.: 20608

Bravo AF: 0.727

Asia WGS AF: 0.669 AC: 2316 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.50
DANN	Benign	0.54
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs10784000; hg19: chr12-60180964;