1-110373396-T-C

Variant names:

• chr1-110373396-T-C
• rs6673423
• NM_004696.3:c.1336+2062A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004696.3. 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
	SLC16A4	NM_004696.3	MANE Select	c.1336+2062A>G		intron	N/A	NP_004687.1	O15374-1
	SLC16A4	NM_001201546.2		c.1192+2062A>G		intron	N/A	NP_001188475.1	O15374-5
	SLC16A4	NM_001201547.2		c.1150+2062A>G		intron	N/A	NP_001188476.1	O15374-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC16A4	ENST00000369779.9	TSL:1 MANE Select	c.1336+2062A>G		intron	N/A	ENSP00000358794.4	O15374-1
	SLC16A4	ENST00000472422.6	TSL:1	c.1192+2062A>G		intron	N/A	ENSP00000432495.1	O15374-5
	SLC16A4	ENST00000369781.8	TSL:1	c.832+2062A>G		intron	N/A	ENSP00000358796.4	O15374-3

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

African (AFR) AF: 0.887 AC: 36791 AN: 41474

American (AMR) AF: 0.800 AC: 12214 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.688 AC: 2387 AN: 3472

East Asian (EAS) AF: 0.750 AC: 3877 AN: 5166

South Asian (SAS) AF: 0.796 AC: 3834 AN: 4818

European-Finnish (FIN) AF: 0.676 AC: 7124 AN: 10540

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.727 AC: 49398 AN: 67958

Other (OTH) AF: 0.744 AC: 1568 AN: 2108

Alfa AF: 0.771 Hom.: 6379

Bravo AF: 0.788

Asia WGS AF: 0.758 AC: 2635 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.72
PhyloP100		-1.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs6673423; hg19: chr1-110916018; COSMIC: COSV63916195; COSMIC: COSV63916195;