chr3-158796571-T-A

Position:

• chr3-158796571-T-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MFSD1	ENST00000465739.5	c.-56-7748T>A		intron_variant		5
MFSD1	ENST00000486568.5	c.116-7748T>A		intron_variant		4
MFSD1	ENST00000491804.1	c.203-7748T>A		intron_variant		5

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

Gnomad4 AFR AF: 0.707

Gnomad4 AMR AF: 0.525

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.355

Gnomad4 SAS AF: 0.602

Gnomad4 FIN AF: 0.541

Gnomad4 NFE AF: 0.551

Gnomad4 OTH AF: 0.591

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6802315; hg19: chr3-158514360;