1-110373396-T-C

Position:

• chr1-110373396-T-C

Variant summary

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

The NM_004696.3(SLC16A4):​c.1336+2062A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.776 in 152,012 control chromosomes in the GnomAD database, including 46,249 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 0.78 (46249 hom., cov: 30)
• Consequence: SLC16A4 NM_004696.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

Genes affected

SLC16A4 (HGNC:10925): (solute carrier family 16 member 4) Predicted to enable monocarboxylic acid transmembrane transporter activity. Predicted to be involved in monocarboxylic acid transport. Predicted to be located in membrane. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

LAMTOR5-AS1 (HGNC:40823): (LAMTOR5 and SLC16A4 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC16A4	NM_004696.3	c.1336+2062A>G		intron_variant		ENST00000369779.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC16A4	ENST00000369779.9	c.1336+2062A>G		intron_variant		1	NM_004696.3	P1
LAMTOR5-AS1	ENST00000626572.2	n.928+17365T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.776 AC: 117890 AN: 151894 Hom.: 46196 Cov.: 30

Gnomad AFR AF: 0.887

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.799

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.796

Gnomad FIN AF: 0.676

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.727

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.776 AC: 118002 AN: 152012 Hom.: 46249 Cov.: 30 AF XY: 0.775 AC XY: 57542 AN XY: 74286

Gnomad4 AFR AF: 0.887

Gnomad4 AMR AF: 0.800

Gnomad4 ASJ AF: 0.688

Gnomad4 EAS AF: 0.750

Gnomad4 SAS AF: 0.796

Gnomad4 FIN AF: 0.676

Gnomad4 NFE AF: 0.727

Gnomad4 OTH AF: 0.744

Alfa AF: 0.766 Hom.: 6073

Bravo AF: 0.788

Asia WGS AF: 0.758 AC: 2635 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.72
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

Publications

LitVar

Other links and lift over

dbSNP: rs6673423; hg19: chr1-110916018; COSMIC: COSV63916195; COSMIC: COSV63916195;