2-24024644-A-G

Variant summary

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

The NM_001346880.2(MFSD2B):c.1490+373A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.547 in 151,904 control chromosomes in the GnomAD database, including 23,132 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 0.55 (23132 hom., cov: 30)
• Consequence: MFSD2B NM_001346880.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.644

Genes affected

MFSD2B (HGNC:37207): (MFSD2 lysolipid transporter B, sphingolipid) Enables sphingolipid transporter activity. Involved in lipid transport. Is integral component of plasma 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MFSD2B	NM_001346880.2	c.1490+373A>G		intron_variant		ENST00000338315.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MFSD2B	ENST00000338315.6	c.1490+373A>G		intron_variant		5	NM_001346880.2	P2
MFSD2B	ENST00000469562.1	n.1269+373A>G		intron_variant, non_coding_transcript_variant		1
MFSD2B	ENST00000669179.1	c.1574+373A>G		intron_variant				A2
MFSD2B	ENST00000453731.1	c.119+373A>G		intron_variant, NMD_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83110 AN: 151786 Hom.: 23119 Cov.: 30

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.547 AC: 83163 AN: 151904 Hom.: 23132 Cov.: 30 AF XY: 0.551 AC XY: 40916 AN XY: 74232

Gnomad4 AFR AF: 0.490

Gnomad4 AMR AF: 0.663

Gnomad4 ASJ AF: 0.579

Gnomad4 EAS AF: 0.818

Gnomad4 SAS AF: 0.501

Gnomad4 FIN AF: 0.530

Gnomad4 NFE AF: 0.539

Gnomad4 OTH AF: 0.583

Alfa AF: 0.547 Hom.: 34876

Bravo AF: 0.558

Asia WGS AF: 0.659 AC: 2288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.039
Dann	Benign	0.35

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7561273; hg19: chr2-24247514;