rs2540317

Variant names:

• chr2-102733348-A-G
• rs2540317
• NM_032718.5:c.166-939T>C

Your query was ambiguous. Multiple possible variants found:

• chr2-102733348-A-G
• chr2-102733348-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032718.5(SLC67A2):​c.166-939T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 152,130 control chromosomes in the GnomAD database, including 3,918 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 0.23 (3918 hom., cov: 32)
• Consequence: SLC67A2 NM_032718.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303
• Publications: 11 publications found

Genes affected

SLC67A2 (HGNC:28158): (major facilitator superfamily domain containing 9) 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032718.5. 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
	SLC67A2	NM_032718.5	MANE Select	c.166-939T>C		intron	N/A	NP_116107.3
	SLC67A2	NM_001322080.2		c.-18-939T>C		intron	N/A	NP_001309009.1	B4DKY6
	SLC67A2	NM_001322081.2		c.-35-922T>C		intron	N/A	NP_001309010.1	B4DKY6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MFSD9	ENST00000258436.10	TSL:1 MANE Select	c.166-939T>C		intron	N/A	ENSP00000258436.5	Q8NBP5
	MFSD9	ENST00000411991.5	TSL:1	n.166-939T>C		intron	N/A	ENSP00000392605.1	F2Z2A2
	MFSD9	ENST00000939979.1		c.166-939T>C		intron	N/A	ENSP00000610038.1

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34546 AN: 152012 Hom.: 3913 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.280

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.235

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.227 AC: 34567 AN: 152130 Hom.: 3918 Cov.: 32 AF XY: 0.225 AC XY: 16722 AN XY: 74364

African (AFR) AF: 0.258 AC: 10727 AN: 41498

American (AMR) AF: 0.206 AC: 3150 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 814 AN: 3470

East Asian (EAS) AF: 0.213 AC: 1101 AN: 5164

South Asian (SAS) AF: 0.255 AC: 1227 AN: 4812

European-Finnish (FIN) AF: 0.175 AC: 1852 AN: 10592

Middle Eastern (MID) AF: 0.267 AC: 78 AN: 292

European-Non Finnish (NFE) AF: 0.219 AC: 14916 AN: 67986

Other (OTH) AF: 0.233 AC: 492 AN: 2114

Alfa AF: 0.201 Hom.: 1895

Bravo AF: 0.229

Asia WGS AF: 0.240 AC: 836 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.6
DANN	Benign	0.42
PhyloP100		0.30
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: rs2540317; hg19: chr2-103349807;