rs955916

Positions:

• chr2-102735320-A-G

Variant summary

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

The NM_032718.5(MFSD9):​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: MFSD9 NM_032718.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.197

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MFSD9	NM_032718.5	c.165+1326T>C		intron_variant		ENST00000258436.10	NP_116107.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MFSD9	ENST00000258436.10	c.165+1326T>C		intron_variant		1	NM_032718.5	ENSP00000258436	P1

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

Gnomad4 AFR AF: 0.640

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.387

Gnomad4 EAS AF: 0.419

Gnomad4 SAS AF: 0.422

Gnomad4 FIN AF: 0.428

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.426

Alfa AF: 0.425 Hom.: 1819

Bravo AF: 0.466

Asia WGS AF: 0.411 AC: 1434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.0
DANN	Benign	0.50

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: rs955916; hg19: chr2-103351779;