chr4-163887873-G-T

Variant names:

• chr4-163887873-G-T
• rs10023694
• NM_001394959.1:c.-38-33704C>A

Variant summary

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

The NM_001394959.1(MARCHF1):​c.-38-33704C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 152,008 control chromosomes in the GnomAD database, including 4,737 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 0.25 (4737 hom., cov: 32)
• Consequence: MARCHF1 NM_001394959.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.192
• Publications: 3 publications found

Genes affected

MARCHF1 (HGNC:26077): (membrane associated ring-CH-type finger 1) MARCH1 is a member of the MARCH family of membrane-bound E3 ubiquitin ligases (EC 6.3.2.19). MARCH proteins add ubiquitin (see MIM 191339) to target lysines in substrate proteins, thereby signaling their vesicular transport between membrane compartments. MARCH1 downregulates the surface expression of major histocompatibility complex (MHC) class II molecules (see MIM 142880) and other glycoproteins by directing them to the late endosomal/lysosomal compartment (Bartee et al., 2004 [PubMed 14722266]; Thibodeau et al., 2008 [PubMed 18389477]; De Gassart et al., 2008 [PubMed 18305173]).[supplied by OMIM, Mar 2010]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001394959.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MARCHF1	NM_001394959.1	MANE Select	c.-38-33704C>A		intron	N/A	NP_001381888.1
	MARCHF1	NM_001166373.2		c.-38-33704C>A		intron	N/A	NP_001159845.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MARCHF1	ENST00000514618.6	TSL:5 MANE Select	c.-38-33704C>A		intron	N/A	ENSP00000421322.1
	MARCHF1	ENST00000503008.5	TSL:1	c.-38-33704C>A		intron	N/A	ENSP00000427223.1
	MARCHF1	ENST00000507270.5	TSL:4	c.-38-33704C>A		intron	N/A	ENSP00000426731.1

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37322 AN: 151886 Hom.: 4740 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.246 AC: 37334 AN: 152008 Hom.: 4737 Cov.: 32 AF XY: 0.248 AC XY: 18398 AN XY: 74328

African (AFR) AF: 0.265 AC: 10988 AN: 41450

American (AMR) AF: 0.204 AC: 3120 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 703 AN: 3470

East Asian (EAS) AF: 0.229 AC: 1185 AN: 5172

South Asian (SAS) AF: 0.313 AC: 1509 AN: 4824

European-Finnish (FIN) AF: 0.311 AC: 3288 AN: 10568

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15797 AN: 67942

Other (OTH) AF: 0.218 AC: 459 AN: 2110

Alfa AF: 0.243 Hom.: 757

Bravo AF: 0.240

Asia WGS AF: 0.241 AC: 840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.61
DANN	Benign	0.64
PhyloP100		-0.19
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10023694; hg19: chr4-164809025;