chr3-183306496-C-G

Position:

• chr3-183306496-C-G

Variant summary

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

The NM_015078.4(MCF2L2):​c.1113+3220G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 152,052 control chromosomes in the GnomAD database, including 5,616 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 0.26 (5616 hom., cov: 32)
• Consequence: MCF2L2 NM_015078.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.180

Genes affected

MCF2L2 (HGNC:30319): (MCF.2 cell line derived transforming sequence-like 2) Predicted to enable guanyl-nucleotide exchange factor activity. Predicted to be involved in regulation of catalytic activity. [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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MCF2L2	NM_015078.4	c.1113+3220G>C		intron_variant		ENST00000328913.8	NP_055893.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MCF2L2	ENST00000328913.8	c.1113+3220G>C		intron_variant		5	NM_015078.4	ENSP00000328118	A2

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39817 AN: 151932 Hom.: 5616 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.262 AC: 39827 AN: 152052 Hom.: 5616 Cov.: 32 AF XY: 0.259 AC XY: 19241 AN XY: 74316

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.349

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.254

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.295

Alfa AF: 0.298 Hom.: 878

Bravo AF: 0.259

Asia WGS AF: 0.171 AC: 594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.64

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: rs35368790; hg19: chr3-183024284;