3-183190077-T-C

Position:

• chr3-183190077-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.3016+2922A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.688 in 152,116 control chromosomes in the GnomAD database, including 37,517 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 0.69 (37517 hom., cov: 32)
• Consequence: MCF2L2 NM_015078.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.157

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]

MCF2L2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MCF2L2	NM_015078.4	c.3016+2922A>G		intron_variant		ENST00000328913.8	NP_055893.4
MCF2L2	XM_011512585.3	c.1957+2922A>G		intron_variant			XP_011510887.1
MCF2L2	XM_047447751.1	c.1915+2922A>G		intron_variant			XP_047303707.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MCF2L2	ENST00000328913.8	c.3016+2922A>G		intron_variant		5	NM_015078.4	ENSP00000328118.3
MCF2L2	ENST00000473233.5	c.3016+2922A>G		intron_variant		5		ENSP00000420070.1
MCF2L2	ENST00000468976.5	n.397+2922A>G		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.689 AC: 104692 AN: 151998 Hom.: 37512 Cov.: 32

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.798

Gnomad AMR AF: 0.711

Gnomad ASJ AF: 0.845

Gnomad EAS AF: 0.839

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.783

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.775

Gnomad OTH AF: 0.711

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

GnomAD4 genome AF: 0.688 AC: 104724 AN: 152116 Hom.: 37517 Cov.: 32 AF XY: 0.691 AC XY: 51368 AN XY: 74328

Gnomad4 AFR AF: 0.474

Gnomad4 AMR AF: 0.711

Gnomad4 ASJ AF: 0.845

Gnomad4 EAS AF: 0.838

Gnomad4 SAS AF: 0.729

Gnomad4 FIN AF: 0.783

Gnomad4 NFE AF: 0.775

Gnomad4 OTH AF: 0.712

Alfa AF: 0.752 Hom.: 42843

Bravo AF: 0.674

Asia WGS AF: 0.757 AC: 2628 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.55

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: rs534333; hg19: chr3-182907865;