rs4907479

Variant names:

• chr13-113004794-G-A
• rs4907479
• NM_001112732.3:c.80-9969G>A

Your query was ambiguous. Multiple possible variants found:

• chr13-113004794-G-A
• chr13-113004794-G-C
• chr13-113004794-G-T

Variant summary

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

The NM_001438390.1(MCF2L):​c.179-9969G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 152,186 control chromosomes in the GnomAD database, including 4,445 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 0.24 (4445 hom., cov: 33)
• Consequence: MCF2L NM_001438390.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 16 publications found

Genes affected

MCF2L (HGNC:14576): (MCF.2 cell line derived transforming sequence like) This gene encodes a guanine nucleotide exchange factor that interacts specifically with the GTP-bound Rac1 and plays a role in the Rho/Rac signaling pathways. A variant in this gene was associated with osteoarthritis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]

LOC107984591 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001438390.1. 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
	MCF2L	NM_001112732.3	MANE Select	c.80-9969G>A		intron	N/A	NP_001106203.2
	MCF2L	NM_001438390.1		c.179-9969G>A		intron	N/A	NP_001425319.1
	MCF2L	NM_001438391.1		c.170-9969G>A		intron	N/A	NP_001425320.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MCF2L	ENST00000535094.7	TSL:2 MANE Select	c.80-9969G>A		intron	N/A	ENSP00000440374.2
	MCF2L	ENST00000421756.5	TSL:1	c.92-9969G>A		intron	N/A	ENSP00000397285.1
	MCF2L	ENST00000375597.8	TSL:1	c.73+2811G>A		intron	N/A	ENSP00000364747.4

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36138 AN: 152068 Hom.: 4439 Cov.: 33

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.238 AC: 36185 AN: 152186 Hom.: 4445 Cov.: 33 AF XY: 0.240 AC XY: 17877 AN XY: 74374

African (AFR) AF: 0.171 AC: 7106 AN: 41552

American (AMR) AF: 0.268 AC: 4096 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 785 AN: 3472

East Asian (EAS) AF: 0.324 AC: 1673 AN: 5160

South Asian (SAS) AF: 0.237 AC: 1142 AN: 4824

European-Finnish (FIN) AF: 0.295 AC: 3121 AN: 10580

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17472 AN: 67994

Other (OTH) AF: 0.233 AC: 492 AN: 2114

Alfa AF: 0.250 Hom.: 10033

Bravo AF: 0.235

Asia WGS AF: 0.276 AC: 963 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.5
DANN	Benign	0.47
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4907479; hg19: chr13-113659108;