2-102716131-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032718.5(MFSD9):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: MFSD9 NM_032718.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

Genes affected

MFSD9 (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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
MFSD9	NM_032718.5	c.*2289A>C		3_prime_UTR_variant	6/6	ENST00000258436.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MFSD9	ENST00000258436.10	c.*2289A>C		3_prime_UTR_variant	6/6	1	NM_032718.5	P1
MFSD9	ENST00000496253.1	n.146-90A>C		intron_variant, non_coding_transcript_variant		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

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

Gnomad4 AFR AF: 0.383

Gnomad4 AMR AF: 0.483

Gnomad4 ASJ AF: 0.486

Gnomad4 EAS AF: 0.763

Gnomad4 SAS AF: 0.665

Gnomad4 FIN AF: 0.629

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.464

Alfa AF: 0.470 Hom.: 9652

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs1051783; hg19: chr2-103332590;