ENST00000486568.5:c.116-7748T>A

Variant names:

• chr3-158796571-T-A
• rs6802315
• ENST00000486568.5:c.116-7748T>A

Variant summary

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

The ENST00000486568.5(MFSD1):​c.116-7748T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.587 in 152,048 control chromosomes in the GnomAD database, including 26,701 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 0.59 (26701 hom., cov: 33)
• Consequence: MFSD1 ENST00000486568.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.671
• Publications: 6 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.7 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MFSD1	ENST00000486568.5	c.116-7748T>A		intron_variant	Intron 1 of 4	4		ENSP00000417414.1
MFSD1	ENST00000491804.1	c.203-7748T>A		intron_variant	Intron 2 of 2	5		ENSP00000420699.1
MFSD1	ENST00000465739.5	c.-56-7748T>A		intron_variant	Intron 1 of 2	5		ENSP00000418055.1

Frequencies

GnomAD3 genomes AF: 0.586 AC: 89077 AN: 151930 Hom.: 26658 Cov.: 33

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.587 AC: 89178 AN: 152048 Hom.: 26701 Cov.: 33 AF XY: 0.586 AC XY: 43541 AN XY: 74314

African (AFR) AF: 0.707 AC: 29327 AN: 41486

American (AMR) AF: 0.525 AC: 8025 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1836 AN: 3468

East Asian (EAS) AF: 0.355 AC: 1834 AN: 5160

South Asian (SAS) AF: 0.602 AC: 2902 AN: 4820

European-Finnish (FIN) AF: 0.541 AC: 5706 AN: 10556

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.551 AC: 37460 AN: 67952

Other (OTH) AF: 0.591 AC: 1249 AN: 2114

Alfa AF: 0.572 Hom.: 3124

Bravo AF: 0.589

Asia WGS AF: 0.546 AC: 1897 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.40
DANN	Benign	0.17
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs6802315; hg19: chr3-158514360;