rs7617304

chr3-158745312-G-A

Variant summary

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

The NR_171782.1(LOC100287290):n.448+3168G>A variant causes a intron, non coding transcript 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: LOC100287290 NR_171782.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.884

Genes affected

(HGNC:):

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100287290	NR_171782.1	n.448+3168G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000465477.5	n.482+3168G>A		intron_variant, non_coding_transcript_variant		5
MFSD1	ENST00000486568.5	c.115+12784G>A		intron_variant		4
MFSD1	ENST00000491804.1	c.202+11275G>A		intron_variant		5
	ENST00000468242.5	n.431+3168G>A		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.183

Gnomad4 ASJ AF: 0.262

Gnomad4 EAS AF: 0.0139

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.0958

Gnomad4 NFE AF: 0.222

Gnomad4 OTH AF: 0.239

Alfa AF: 0.227 Hom.: 8449

Bravo AF: 0.232

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	5.0
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7617304; hg19: chr3-158463101;