rs1664425608

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr1-155135960-G-C
• chr1-155135960-G-A
• chr1-155135960-G-T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 2P and 6B. PM2 BP4_Strong BP6_Moderate

The NM_018845.4(SLC50A1):​c.49G>C​(p.Val17Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000479 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. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 0.0000048 (0 hom.)
• Consequence: SLC50A1 NM_018845.4 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• 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 -4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.036250263).
• BP6: Variant 1-155135960-G-C is Benign according to our data. Variant chr1-155135960-G-C is described in ClinVar as Likely_benign. ClinVar VariationId is 3320006.Status of the report is criteria_provided_single_submitter, 1 stars.

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>C	p.Val17Leu	missense	Exon 1 of 6	NP_061333.2	Q9BRV3-1
	SLC50A1	NM_001287587.2		c.8G>C	p.Gly3Ala	missense	Exon 1 of 6	NP_001274516.1
	SLC50A1	NM_001287586.2		c.8G>C	p.Gly3Ala	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>C	p.Val17Leu	missense	Exon 1 of 6	ENSP00000357389.4	Q9BRV3-1
	SLC50A1	ENST00000303343.12	TSL:1	c.49G>C	p.Val17Leu	missense	Exon 1 of 5	ENSP00000306146.8	Q9BRV3-3
	SLC50A1	ENST00000368401.6	TSL:1	c.8G>C	p.Gly3Ala	missense	Exon 1 of 5	ENSP00000357386.5	Q9BRV3-2

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 0.00000479 AC: 7 AN: 1461796 Hom.: 0 Cov.: 35 AF XY: 0.00000413 AC XY: 3 AN XY: 727186

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

American (AMR) AF: 0.000134 AC: 6 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: 0.00 AC: 0 AN: 1111996

Other (OTH) AF: 0.0000166 AC: 1 AN: 60394

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.0000113

ClinVar

ClinVar submissions

Significance: Likely benign

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	0.13
BayesDel_addAF	Uncertain	0.020	T
BayesDel_noAF	Benign	-0.68
CADD	Benign	10
DANN	Benign	0.90
DEOGEN2	Benign	0.010	T
Eigen	Benign	-0.70
Eigen_PC	Benign	-0.63
FATHMM_MKL	Benign	0.49	N
LIST_S2	Benign	0.37	T
M_CAP	Benign	0.046	D
MetaRNN	Benign	0.036	T
MetaSVM	Benign	-0.99	T
PhyloP100		-0.25
PROVEAN	Benign	0.83	N
REVEL	Benign	0.065
Sift	Pathogenic	0.0	D
Polyphen		0.0	B
Vest4		0.092
MutPred		0.19		Loss of methylation at R2 (P = 0.1108)
MVP		0.040
ClinPred		0.082	T
GERP RS		-1.3
PromoterAI		-0.067	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.081
Mutation Taster		=85/15	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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;