1-112956453-G-C

Position:

• chr1-112956453-G-C

Variant summary

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

The NR_103743.1(SLC16A1-AS1):​n.39G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00656 in 335,064 control chromosomes in the GnomAD database, including 86 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 0.0035 (16 hom., cov: 31)
  • Exomes 𝑓: 0.0091 (70 hom.)
• Consequence: SLC16A1-AS1 NR_103743.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06

Genes affected

SLC16A1-AS1 (HGNC:49445): (SLC16A1 antisense RNA 1)

SLC16A1 (HGNC:10922): (solute carrier family 16 member 1) The protein encoded by this gene is a proton-linked monocarboxylate transporter that catalyzes the movement of many monocarboxylates, such as lactate and pyruvate, across the plasma membrane. Mutations in this gene are associated with erythrocyte lactate transporter defect. Alternatively spliced transcript variants have been found for this gene.[provided by RefSeq, Oct 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0608 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC16A1-AS1	NR_103743.1	n.39G>C		non_coding_transcript_exon_variant	1/3
SLC16A1-AS1	NR_103744.1	n.39G>C		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC16A1-AS1	ENST00000416193.6	n.39G>C		non_coding_transcript_exon_variant	1/3	1
SLC16A1-AS1	ENST00000428411.6	n.39G>C		non_coding_transcript_exon_variant	1/3	1
SLC16A1	ENST00000429288.2	c.-45+386C>G		intron_variant		3		ENSP00000397106	P1

Frequencies

GnomAD3 genomes AF: 0.00351 AC: 534 AN: 152022 Hom.: 16 Cov.: 31

Gnomad AFR AF: 0.000193

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00688

Gnomad ASJ AF: 0.00778

Gnomad EAS AF: 0.0666

Gnomad SAS AF: 0.00580

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000250

Gnomad OTH AF: 0.00336

GnomAD4 exome AF: 0.00910 AC: 1665 AN: 182924 Hom.: 70 Cov.: 0 AF XY: 0.00867 AC XY: 808 AN XY: 93244

Gnomad4 AFR exome AF: 0.000758

Gnomad4 AMR exome AF: 0.00746

Gnomad4 ASJ exome AF: 0.00915

Gnomad4 EAS exome AF: 0.0835

Gnomad4 SAS exome AF: 0.00122

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000380

Gnomad4 OTH exome AF: 0.00527

GnomAD4 genome AF: 0.00351 AC: 534 AN: 152140 Hom.: 16 Cov.: 31 AF XY: 0.00399 AC XY: 297 AN XY: 74378

Gnomad4 AFR AF: 0.000193

Gnomad4 AMR AF: 0.00694

Gnomad4 ASJ AF: 0.00778

Gnomad4 EAS AF: 0.0666

Gnomad4 SAS AF: 0.00581

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000250

Gnomad4 OTH AF: 0.00332

Alfa AF: 0.000108 Hom.: 0

Bravo AF: 0.00431

Asia WGS AF: 0.0310 AC: 107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.5
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs60844753; hg19: chr1-113499075;