13-77040302-T-C

Variant names:

• chr13-77040302-T-C
• rs424391
• ENST00000638147.2:c.566-35216T>C

Variant summary

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

The ENST00000638147.2(ENSG00000283208):​c.566-35216T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.64 in 151,974 control chromosomes in the GnomAD database, including 34,383 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 0.64 (34383 hom., cov: 31)
• Consequence: ENSG00000283208 ENST00000638147.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.542
• Publications: 2 publications found

Genes affected

ENSG00000283208 (HGNC:):

MYCBP2-AS1 (HGNC:41023): (MYCBP2 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000638147.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000283208	ENST00000638147.2	TSL:5	c.566-35216T>C		intron	N/A	ENSP00000490953.2	A0A1B0GWJ7
	ENSG00000283208	ENST00000638101.1	TSL:5	c.169+44175T>C		intron	N/A	ENSP00000490535.1	A0A1B0GVJ0
	ENSG00000283208	ENST00000635838.1	TSL:5	c.173-35216T>C		intron	N/A	ENSP00000490835.1	A0A1B0GW94

Frequencies

GnomAD3 genomes AF: 0.640 AC: 97241 AN: 151856 Hom.: 34384 Cov.: 31

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.813

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.771

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.797

Gnomad OTH AF: 0.677

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

GnomAD4 genome AF: 0.640 AC: 97257 AN: 151974 Hom.: 34383 Cov.: 31 AF XY: 0.637 AC XY: 47307 AN XY: 74290

African (AFR) AF: 0.335 AC: 13900 AN: 41452

American (AMR) AF: 0.712 AC: 10865 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.813 AC: 2823 AN: 3472

East Asian (EAS) AF: 0.483 AC: 2485 AN: 5146

South Asian (SAS) AF: 0.547 AC: 2627 AN: 4800

European-Finnish (FIN) AF: 0.771 AC: 8128 AN: 10548

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.797 AC: 54177 AN: 67968

Other (OTH) AF: 0.674 AC: 1423 AN: 2112

Alfa AF: 0.692 Hom.: 7424

Bravo AF: 0.626

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.44
DANN	Benign	0.60
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs424391; hg19: chr13-77614437;