3-186827530-C-T

Variant names:

• chr3-186827530-C-T
• rs58575091
• ENST00000702187.2:n.40G>A

Variant summary

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

The ENST00000702187.2(ENSG00000289971):​n.40G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 152,084 control chromosomes in the GnomAD database, including 15,862 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 0.45 (15862 hom., cov: 35)
• Consequence: ENSG00000289971 ENST00000702187.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77
• Publications: 3 publications found

Genes affected

ENSG00000289971 (HGNC:):

MCF2L2P1 (HGNC:56615): (MCF2L2 pseudogene 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289971	ENST00000702187.2	n.40G>A		non_coding_transcript_exon_variant	Exon 1 of 1
MCF2L2P1	ENST00000448639.1	n.*193C>T		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68345 AN: 151976 Hom.: 15859 Cov.: 35

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.450 AC: 68377 AN: 152084 Hom.: 15862 Cov.: 35 AF XY: 0.454 AC XY: 33730 AN XY: 74340

African (AFR) AF: 0.358 AC: 14860 AN: 41518

American (AMR) AF: 0.471 AC: 7200 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1441 AN: 3466

East Asian (EAS) AF: 0.447 AC: 2285 AN: 5114

South Asian (SAS) AF: 0.476 AC: 2301 AN: 4832

European-Finnish (FIN) AF: 0.610 AC: 6474 AN: 10608

Middle Eastern (MID) AF: 0.329 AC: 96 AN: 292

European-Non Finnish (NFE) AF: 0.477 AC: 32387 AN: 67938

Other (OTH) AF: 0.402 AC: 848 AN: 2112

Alfa AF: 0.364 Hom.: 1076

Bravo AF: 0.435

Asia WGS AF: 0.479 AC: 1660 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.3
DANN	Benign	0.88
PhyloP100		-1.8

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs58575091; hg19: chr3-186545319;