ENST00000486568.5:c.115+12784G>A

Variant names:

• chr3-158745312-G-A
• rs7617304
• ENST00000486568.5:c.115+12784G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000486568.5(MFSD1):​c.115+12784G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 152,076 control chromosomes in the GnomAD database, including 4,228 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 (4228 hom., cov: 32)
• Consequence: MFSD1 ENST00000486568.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.884
• Publications: 13 publications found

Genes affected

MFSD1 (HGNC:25874): (major facilitator superfamily domain containing 1) Predicted to enable protein homodimerization activity. Predicted to be involved in protein localization to lysosome and protein stabilization. Predicted to be located in lysosome. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000240207 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000486568.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC100287290	NR_171782.1		n.448+3168G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MFSD1	ENST00000486568.5	TSL:4	c.115+12784G>A		intron	N/A	ENSP00000417414.1
	MFSD1	ENST00000491804.1	TSL:5	c.202+11275G>A		intron	N/A	ENSP00000420699.1
	ENSG00000240207	ENST00000465477.6	TSL:5	n.482+3168G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34295 AN: 151958 Hom.: 4228 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.0139

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.0958

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.226 AC: 34317 AN: 152076 Hom.: 4228 Cov.: 32 AF XY: 0.219 AC XY: 16297 AN XY: 74354

African (AFR) AF: 0.301 AC: 12494 AN: 41446

American (AMR) AF: 0.183 AC: 2803 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 908 AN: 3472

East Asian (EAS) AF: 0.0139 AC: 72 AN: 5180

South Asian (SAS) AF: 0.225 AC: 1086 AN: 4820

European-Finnish (FIN) AF: 0.0958 AC: 1016 AN: 10600

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.222 AC: 15066 AN: 67970

Other (OTH) AF: 0.239 AC: 504 AN: 2110

Alfa AF: 0.227 Hom.: 17561

Bravo AF: 0.232

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.0
DANN	Benign	0.70
PhyloP100		0.88

Splicing

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

Other links and lift over

dbSNP: rs7617304; hg19: chr3-158463101;