2-102716131-T-G

Variant names:

• chr2-102716131-T-G
• rs1051783
• NM_032718.5:c.*2289A>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.*2289A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 151,956 control chromosomes in the GnomAD database, including 18,459 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 0.48 (18459 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: SLC67A2 NM_032718.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 6 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 (EAS) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC67A2	NM_032718.5	c.*2289A>C		3_prime_UTR_variant	Exon 6 of 6	ENST00000258436.10	NP_116107.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MFSD9	ENST00000258436.10	c.*2289A>C		3_prime_UTR_variant	Exon 6 of 6	1	NM_032718.5	ENSP00000258436.5
MFSD9	ENST00000496253.1	n.146-90A>C		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73333 AN: 151838 Hom.: 18445 Cov.: 32

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.763

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.459

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.483 AC: 73399 AN: 151956 Hom.: 18459 Cov.: 32 AF XY: 0.495 AC XY: 36752 AN XY: 74264

African (AFR) AF: 0.383 AC: 15877 AN: 41442

American (AMR) AF: 0.483 AC: 7375 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1685 AN: 3470

East Asian (EAS) AF: 0.763 AC: 3939 AN: 5164

South Asian (SAS) AF: 0.665 AC: 3200 AN: 4812

European-Finnish (FIN) AF: 0.629 AC: 6630 AN: 10548

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.486 AC: 33048 AN: 67936

Other (OTH) AF: 0.464 AC: 980 AN: 2114

Alfa AF: 0.474 Hom.: 13184

Bravo AF: 0.462

Asia WGS AF: 0.678 AC: 2357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.14
DANN	Benign	0.70
PhyloP100		-1.5
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: rs1051783; hg19: chr2-103332590;