chr16-15603938-C-T

Position:

• chr16-15603938-C-T

Variant summary

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

The NM_014647.4(MARF1):​c.4413+230G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 151,698 control chromosomes in the GnomAD database, including 14,429 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 0.43 (14429 hom., cov: 31)
• Consequence: MARF1 NM_014647.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

Genes affected

MARF1 (HGNC:29562): (meiosis regulator and mRNA stability factor 1) This gene encodes a putative peroxisomal protein that appears to be conserved across Euteleostomi. In humans, it may be autoantigenic. [provided by RefSeq, Jul 2010]

BMERB1 (HGNC:19213): (bMERB domain containing 1) Predicted to act upstream of or within negative regulation of cell motility involved in cerebral cortex radial glia guided migration and negative regulation of microtubule depolymerization. Predicted to be located in microtubule cytoskeleton. [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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MARF1	NM_014647.4	c.4413+230G>A		intron_variant		ENST00000396368.8	NP_055462.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MARF1	ENST00000396368.8	c.4413+230G>A		intron_variant		1	NM_014647.4	ENSP00000379654	P5

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65415 AN: 151580 Hom.: 14420 Cov.: 31

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.431 AC: 65445 AN: 151698 Hom.: 14429 Cov.: 31 AF XY: 0.438 AC XY: 32443 AN XY: 74106

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.484

Gnomad4 ASJ AF: 0.530

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.505

Gnomad4 FIN AF: 0.523

Gnomad4 NFE AF: 0.455

Gnomad4 OTH AF: 0.440

Alfa AF: 0.446 Hom.: 1904

Bravo AF: 0.426

Asia WGS AF: 0.382 AC: 1330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.44

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2071330; hg19: chr16-15697795;