rs925229

Variant names:

• chr2-24011570-A-G
• rs925229
• NM_001346880.2:c.96+1378A>G

Variant summary

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

The NM_001346880.2(MFSD2B):​c.96+1378A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 151,930 control chromosomes in the GnomAD database, including 17,265 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 0.47 (17265 hom., cov: 31)
• Consequence: MFSD2B NM_001346880.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76

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=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.749 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MFSD2B	NM_001346880.2	c.96+1378A>G		intron_variant	Intron 1 of 13	ENST00000338315.6	NP_001333809.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MFSD2B	ENST00000338315.6	c.96+1378A>G		intron_variant	Intron 1 of 13	5	NM_001346880.2	ENSP00000342501.4
MFSD2B	ENST00000669179.1	c.96+1378A>G		intron_variant	Intron 1 of 14			ENSP00000499689.1
MFSD2B	ENST00000406420.7	c.96+1378A>G		intron_variant	Intron 1 of 12	5		ENSP00000385527.3

Frequencies

GnomAD3 genomes AF: 0.469 AC: 71153 AN: 151812 Hom.: 17254 Cov.: 31

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.770

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.469 AC: 71184 AN: 151930 Hom.: 17265 Cov.: 31 AF XY: 0.474 AC XY: 35188 AN XY: 74240

Gnomad4 AFR AF: 0.413

Gnomad4 AMR AF: 0.605

Gnomad4 ASJ AF: 0.477

Gnomad4 EAS AF: 0.769

Gnomad4 SAS AF: 0.460

Gnomad4 FIN AF: 0.436

Gnomad4 NFE AF: 0.451

Gnomad4 OTH AF: 0.492

Alfa AF: 0.458 Hom.: 21630

Bravo AF: 0.483

Asia WGS AF: 0.608 AC: 2110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	0.044
DANN	Benign	0.44

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: rs925229; hg19: chr2-24234440;