rs955916

Variant names:

• chr2-102735320-A-G
• rs955916
• NM_032718.5:c.165+1326T>C

Variant summary

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

The NM_032718.5(SLC67A2):​c.165+1326T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.461 in 152,034 control chromosomes in the GnomAD database, including 17,138 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 0.46 (17138 hom., cov: 32)
• Consequence: SLC67A2 NM_032718.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.197
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.633 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.165+1326T>C		intron	N/A	NP_116107.3
	SLC67A2	NM_001322080.2		c.-19+1210T>C		intron	N/A	NP_001309009.1	B4DKY6
	SLC67A2	NM_001322081.2		c.-36+1326T>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.165+1326T>C		intron	N/A	ENSP00000258436.5	Q8NBP5
	MFSD9	ENST00000411991.5	TSL:1	n.165+1326T>C		intron	N/A	ENSP00000392605.1	F2Z2A2
	MFSD9	ENST00000939979.1		c.165+1326T>C		intron	N/A	ENSP00000610038.1

Frequencies

GnomAD3 genomes AF: 0.461 AC: 70054 AN: 151916 Hom.: 17113 Cov.: 32

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.461 AC: 70124 AN: 152034 Hom.: 17138 Cov.: 32 AF XY: 0.460 AC XY: 34151 AN XY: 74306

African (AFR) AF: 0.640 AC: 26518 AN: 41464

American (AMR) AF: 0.394 AC: 6019 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1343 AN: 3466

East Asian (EAS) AF: 0.419 AC: 2168 AN: 5176

South Asian (SAS) AF: 0.422 AC: 2026 AN: 4802

European-Finnish (FIN) AF: 0.428 AC: 4519 AN: 10554

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.385 AC: 26199 AN: 67972

Other (OTH) AF: 0.426 AC: 897 AN: 2104

Alfa AF: 0.433 Hom.: 1959

Bravo AF: 0.466

Asia WGS AF: 0.411 AC: 1434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.0
DANN	Benign	0.50
PhyloP100		0.20
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: rs955916; hg19: chr2-103351779;