rs4907479

Positions:

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

Variant summary

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

The NM_001112732.3(MCF2L):​c.80-9969G>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_001112732.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MCF2L	NM_001112732.3	c.80-9969G>A		intron_variant		ENST00000535094.7	NP_001106203.2
LOC107984591	XR_001750037.2	n.1703G>A		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MCF2L	ENST00000535094.7	c.80-9969G>A		intron_variant		2	NM_001112732.3	ENSP00000440374	A1

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

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.324

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.295

Gnomad4 NFE AF: 0.257

Gnomad4 OTH AF: 0.233

Alfa AF: 0.233 Hom.: 2393

Bravo AF: 0.235

Asia WGS AF: 0.276 AC: 963 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.5
DANN	Benign	0.47

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: rs4907479; hg19: chr13-113659108;