chr2-24024644-A-G

Variant names:

• chr2-24024644-A-G
• rs7561273
• NM_001346880.2:c.1490+373A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 36 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001346880.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MFSD2B	NM_001346880.2	MANE Select	c.1490+373A>G		intron	N/A	NP_001333809.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MFSD2B	ENST00000338315.6	TSL:5 MANE Select	c.1490+373A>G		intron	N/A	ENSP00000342501.4
	MFSD2B	ENST00000469562.1	TSL:1	n.1269+373A>G		intron	N/A
	MFSD2B	ENST00000669179.1		c.1574+373A>G		intron	N/A	ENSP00000499689.1

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

African (AFR) AF: 0.490 AC: 20306 AN: 41420

American (AMR) AF: 0.663 AC: 10119 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.579 AC: 2008 AN: 3468

East Asian (EAS) AF: 0.818 AC: 4224 AN: 5162

South Asian (SAS) AF: 0.501 AC: 2408 AN: 4804

European-Finnish (FIN) AF: 0.530 AC: 5593 AN: 10562

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.539 AC: 36598 AN: 67906

Other (OTH) AF: 0.583 AC: 1231 AN: 2112

Alfa AF: 0.548 Hom.: 80171

Bravo AF: 0.558

Asia WGS AF: 0.659 AC: 2288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.039
DANN	Benign	0.35
PhyloP100		-0.64
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs7561273; hg19: chr2-24247514;