rs779346651

Variant names:

• chr1-94827562-C-G
• rs779346651
• NM_001114106.3:c.334C>G

Your query was ambiguous. Multiple possible variants found:

• chr1-94827562-C-G
• chr1-94827562-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001114106.3(SLC44A3):​c.334C>G​(p.Arg112Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R112C) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SLC44A3 NM_001114106.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.38
• Publications: 3 publications found

Genes affected

SLC44A3 (HGNC:28689): (solute carrier family 44 member 3) Predicted to enable transmembrane transporter activity. Predicted to be involved in transmembrane transport. Predicted to be located in plasma membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Apr 2022]

SLC44A3-AS1 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.11782211).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001114106.3. 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
	SLC44A3	NM_001114106.3	MANE Select	c.334C>G	p.Arg112Gly	missense	Exon 4 of 15	NP_001107578.1	Q8N4M1-1
	SLC44A3	NM_001258340.2		c.334C>G	p.Arg112Gly	missense	Exon 4 of 15	NP_001245269.1
	SLC44A3	NM_001258342.2		c.226C>G	p.Arg76Gly	missense	Exon 3 of 14	NP_001245271.1	Q8N4M1-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC44A3	ENST00000271227.11	TSL:1 MANE Select	c.334C>G	p.Arg112Gly	missense	Exon 4 of 15	ENSP00000271227.6	Q8N4M1-1
	SLC44A3	ENST00000467909.5	TSL:1	c.190C>G	p.Arg64Gly	missense	Exon 3 of 14	ENSP00000432789.1	Q8N4M1-2
	SLC44A3	ENST00000475883.5	TSL:1	n.*57C>G		non_coding_transcript_exon	Exon 3 of 14	ENSP00000434457.1	H0YDW5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD2 exomes AF: 0.00000398 AC: 1 AN: 251462 AF XY: 0.00000736

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0000544

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ExAC AF: 0.00000824 AC: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.070
BayesDel_addAF	Benign	-0.22	T
BayesDel_noAF	Benign	-0.39
CADD	Benign	12
DANN	Benign	0.97
DEOGEN2	Benign	0.0084	T
Eigen	Benign	-0.79
Eigen_PC	Benign	-0.74
FATHMM_MKL	Benign	0.48	N
LIST_S2	Benign	0.57	T
M_CAP	Benign	0.034	D
MetaRNN	Benign	0.12	T
MetaSVM	Benign	-0.98	T
MutationAssessor	Benign	0.0	N
PhyloP100		1.4
PrimateAI	Benign	0.25	T
PROVEAN	Benign	0.020	N
REVEL	Benign	0.045
Sift	Uncertain	0.0090	D
Sift4G	Uncertain	0.028	D
Polyphen		0.018	B
Vest4		0.36
MutPred		0.45		Loss of stability (P = 0.0911)
MVP		0.58
MPC		0.20
ClinPred		0.088	T
GERP RS		0.55
Varity_R		0.076
gMVP		0.51
Mutation Taster		=95/5	polymorphism

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: rs779346651; hg19: chr1-95293118;