rs768402677

Variant names:

• chr11-57415095-C-A
• rs768402677
• NM_199329.3:c.781G>T

Your query was ambiguous. Multiple possible variants found:

• chr11-57415095-C-A
• chr11-57415095-C-T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_199329.3(SLC43A3):​c.781G>T​(p.Ala261Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000597 in 1,457,210 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.000060 (0 hom.)
• Consequence: SLC43A3 NM_199329.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.328
• Publications: 0 publications found

Genes affected

SLC43A3 (HGNC:17466): (solute carrier family 43 member 3) Predicted to enable transmembrane transporter activity. Predicted to be involved in transmembrane transport. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000254979 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0096443).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_199329.3. 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
	SLC43A3	NM_199329.3	MANE Select	c.781G>T	p.Ala261Ser	missense	Exon 10 of 14	NP_955361.1	Q8NBI5-1
	SLC43A3	NM_001278206.2		c.820G>T	p.Ala274Ser	missense	Exon 10 of 14	NP_001265135.1	Q8NBI5-2
	SLC43A3	NM_001278201.2		c.781G>T	p.Ala261Ser	missense	Exon 10 of 14	NP_001265130.1	Q8NBI5-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC43A3	ENST00000395124.6	TSL:1 MANE Select	c.781G>T	p.Ala261Ser	missense	Exon 10 of 14	ENSP00000378556.1	Q8NBI5-1
	SLC43A3	ENST00000352187.5	TSL:1	c.781G>T	p.Ala261Ser	missense	Exon 10 of 14	ENSP00000337561.1	Q8NBI5-1
	SLC43A3	ENST00000395123.6	TSL:1	c.781G>T	p.Ala261Ser	missense	Exon 10 of 14	ENSP00000378555.2	Q8NBI5-1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD2 exomes AF: 0.000147 AC: 36 AN: 245720 AF XY: 0.000136

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000597 AC: 87 AN: 1457210 Hom.: 0 Cov.: 32 AF XY: 0.0000745 AC XY: 54 AN XY: 724578

African (AFR) AF: 0.00 AC: 0 AN: 33406

American (AMR) AF: 0.00 AC: 0 AN: 44298

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25618

East Asian (EAS) AF: 0.00 AC: 0 AN: 39694

South Asian (SAS) AF: 0.000902 AC: 77 AN: 85390

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53188

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5738

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1109664

Other (OTH) AF: 0.000166 AC: 10 AN: 60214

GnomAD4 genome Cov.: 32

ExAC AF: 0.000173 AC: 21

Asia WGS AF: 0.00260 AC: 9 AN: 3478

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.070
BayesDel_addAF	Benign	-0.49	T
BayesDel_noAF	Benign	-0.52
CADD	Benign	1.3
DANN	Benign	0.47
DEOGEN2	Benign	0.13	T
Eigen	Benign	-1.9
Eigen_PC	Benign	-1.8
FATHMM_MKL	Benign	0.074	N
LIST_S2	Benign	0.59	T
M_CAP	Benign	0.026	D
MetaRNN	Benign	0.0096	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.90	L
PhyloP100		0.33
PrimateAI	Benign	0.24	T
PROVEAN	Benign	-0.53	N
REVEL	Benign	0.018
Sift	Benign	0.50	T
Sift4G	Benign	0.64	T
Polyphen		0.0010	B
Vest4		0.036
MutPred		0.30		Gain of glycosylation at A261 (P = 0.0082)
MVP		0.12
MPC		0.10
ClinPred		0.019	T
GERP RS		-2.3
RBP_binding_hub_radar		0.97
RBP_regulation_power_radar		2.0
Varity_R		0.080
gMVP		0.24
Mutation Taster		=97/3	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs768402677; hg19: chr11-57182568;