rs7634425

Positions:

• chr3-183302804-T-C

Variant summary

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

The NM_015078.4(MCF2L2):​c.1114-2608A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 151,950 control chromosomes in the GnomAD database, including 6,706 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 0.28 (6706 hom., cov: 31)
• Consequence: MCF2L2 NM_015078.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160

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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MCF2L2	NM_015078.4	c.1114-2608A>G		intron_variant		ENST00000328913.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MCF2L2	ENST00000328913.8	c.1114-2608A>G		intron_variant		5	NM_015078.4	A2

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42712 AN: 151832 Hom.: 6696 Cov.: 31

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.281 AC: 42755 AN: 151950 Hom.: 6706 Cov.: 31 AF XY: 0.285 AC XY: 21172 AN XY: 74256

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.486

Gnomad4 SAS AF: 0.347

Gnomad4 FIN AF: 0.269

Gnomad4 NFE AF: 0.203

Gnomad4 OTH AF: 0.256

Alfa AF: 0.224 Hom.: 8561

Bravo AF: 0.288

Asia WGS AF: 0.419 AC: 1455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.4
DANN	Benign	0.31

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: rs7634425; hg19: chr3-183020592;