1-155135960-G-A

Variant names:

• chr1-155135960-G-A
• rs1664425608
• NM_018845.4:c.49G>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_018845.4(SLC50A1):​c.49G>A​(p.Val17Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,796 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/17 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. V17L) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: SLC50A1 NM_018845.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250
• Publications: 0 publications found

Genes affected

SLC50A1 (HGNC:30657): (solute carrier family 50 member 1) Enables glucoside transmembrane transporter activity. Predicted to be involved in carbohydrate transport. Located in Golgi apparatus and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.05204898).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018845.4. 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
	SLC50A1	NM_018845.4	MANE Select	c.49G>A	p.Val17Ile	missense	Exon 1 of 6	NP_061333.2	Q9BRV3-1
	SLC50A1	NM_001287587.2		c.8G>A	p.Gly3Asp	missense	Exon 1 of 6	NP_001274516.1
	SLC50A1	NM_001287586.2		c.8G>A	p.Gly3Asp	missense	Exon 1 of 5	NP_001274515.1	A0A087WXX5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC50A1	ENST00000368404.9	TSL:1 MANE Select	c.49G>A	p.Val17Ile	missense	Exon 1 of 6	ENSP00000357389.4	Q9BRV3-1
	SLC50A1	ENST00000303343.12	TSL:1	c.49G>A	p.Val17Ile	missense	Exon 1 of 5	ENSP00000306146.8	Q9BRV3-3
	SLC50A1	ENST00000368401.6	TSL:1	c.8G>A	p.Gly3Asp	missense	Exon 1 of 5	ENSP00000357386.5	Q9BRV3-2

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 0.00000137 AC: 2 AN: 1461796 Hom.: 0 Cov.: 35 AF XY: 0.00000138 AC XY: 1 AN XY: 727186

African (AFR) AF: 0.00 AC: 0 AN: 33478

American (AMR) AF: 0.00 AC: 0 AN: 44720

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26134

East Asian (EAS) AF: 0.00 AC: 0 AN: 39700

South Asian (SAS) AF: 0.00 AC: 0 AN: 86254

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53354

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5766

European-Non Finnish (NFE) AF: 0.00000180 AC: 2 AN: 1111996

Other (OTH) AF: 0.00 AC: 0 AN: 60394

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.10
BayesDel_addAF	Uncertain	0.058	T
BayesDel_noAF	Benign	-0.64
CADD	Benign	13
DANN	Benign	0.94
DEOGEN2	Benign	0.027	T
Eigen	Benign	-0.78
Eigen_PC	Benign	-0.70
FATHMM_MKL	Benign	0.62	D
LIST_S2	Benign	0.31	T
M_CAP	Benign	0.059	D
MetaRNN	Benign	0.052	T
MetaSVM	Benign	-0.95	T
PhyloP100		-0.25
PROVEAN	Benign	0.82	N
REVEL	Benign	0.043
Sift	Pathogenic	0.0	D
Polyphen		0.43	B
Vest4		0.18
MutPred		0.22		Loss of MoRF binding (P = 0.0424)
MVP		0.040
ClinPred		0.32	T
GERP RS		-1.3
PromoterAI		0.061	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.042
Mutation Taster		=87/13	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs1664425608; hg19: chr1-155108436;