rs2540317

Positions:

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

Variant summary

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

The NM_032718.5(MFSD9):​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: MFSD9 NM_032718.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303

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 (AFR) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MFSD9	NM_032718.5	c.166-939T>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.166-939T>C		intron_variant		1	NM_032718.5	ENSP00000258436	P1

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

Gnomad4 AFR AF: 0.258

Gnomad4 AMR AF: 0.206

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.213

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.233

Alfa AF: 0.199 Hom.: 1695

Bravo AF: 0.229

Asia WGS AF: 0.240 AC: 836 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	3.6
DANN	Benign	0.42

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: rs2540317; hg19: chr2-103349807;