rs7600852

Variant names:

• chr2-24024816-C-T
• rs7600852
• NM_001346880.2:c.1490+545C>T

Variant summary

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

The NM_001346880.2(MFSD2B):​c.1490+545C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0906 in 152,164 control chromosomes in the GnomAD database, including 673 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 0.091 (673 hom., cov: 31)
• Consequence: MFSD2B NM_001346880.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.20

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=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MFSD2B	NM_001346880.2	c.1490+545C>T		intron_variant	Intron 13 of 13	ENST00000338315.6	NP_001333809.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MFSD2B	ENST00000338315.6	c.1490+545C>T		intron_variant	Intron 13 of 13	5	NM_001346880.2	ENSP00000342501.4
MFSD2B	ENST00000469562.1	n.1269+545C>T		intron_variant	Intron 7 of 7	1
MFSD2B	ENST00000669179.1	c.1574+545C>T		intron_variant	Intron 14 of 14			ENSP00000499689.1
MFSD2B	ENST00000453731.1	n.119+545C>T		intron_variant	Intron 1 of 4	3		ENSP00000390490.1

Frequencies

GnomAD3 genomes AF: 0.0905 AC: 13756 AN: 152046 Hom.: 670 Cov.: 31

Gnomad AFR AF: 0.0902

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.0835

Gnomad ASJ AF: 0.0841

Gnomad EAS AF: 0.0141

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0618

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0978

Gnomad OTH AF: 0.0972

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

GnomAD4 genome AF: 0.0906 AC: 13786 AN: 152164 Hom.: 673 Cov.: 31 AF XY: 0.0890 AC XY: 6624 AN XY: 74386

Gnomad4 AFR AF: 0.0907

Gnomad4 AMR AF: 0.0834

Gnomad4 ASJ AF: 0.0841

Gnomad4 EAS AF: 0.0143

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.0618

Gnomad4 NFE AF: 0.0978

Gnomad4 OTH AF: 0.0967

Alfa AF: 0.0903 Hom.: 164

Bravo AF: 0.0899

Asia WGS AF: 0.0800 AC: 279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.9
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7600852; hg19: chr2-24247686;