1-39891596-A-G

Variant names:

• chr1-39891596-A-G
• rs3131691
• ENST00000418255.2:n.326-6147A>G

Variant summary

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

The ENST00000418255.2(MYCL-AS1):​n.326-6147A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 151,918 control chromosomes in the GnomAD database, including 6,574 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 (6574 hom., cov: 32)
• Consequence: MYCL-AS1 ENST00000418255.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.589
• Publications: 5 publications found

Genes affected

MYCL-AS1 (HGNC:40386): (MYCL antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000418255.2. 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
	MYCL-AS1	NR_183424.1		n.273-6147A>G		intron	N/A
	MYCL-AS1	NR_183425.1		n.36-6147A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYCL-AS1	ENST00000418255.2	TSL:2	n.326-6147A>G		intron	N/A
	MYCL-AS1	ENST00000837551.1		n.304-6147A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42783 AN: 151802 Hom.: 6543 Cov.: 32

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.282 AC: 42869 AN: 151918 Hom.: 6574 Cov.: 32 AF XY: 0.284 AC XY: 21123 AN XY: 74264

African (AFR) AF: 0.403 AC: 16673 AN: 41402

American (AMR) AF: 0.294 AC: 4494 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 925 AN: 3464

East Asian (EAS) AF: 0.296 AC: 1525 AN: 5158

South Asian (SAS) AF: 0.238 AC: 1150 AN: 4822

European-Finnish (FIN) AF: 0.266 AC: 2804 AN: 10546

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.214 AC: 14506 AN: 67938

Other (OTH) AF: 0.274 AC: 579 AN: 2110

Alfa AF: 0.240 Hom.: 5737

Bravo AF: 0.291

Asia WGS AF: 0.306 AC: 1064 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	2.8
DANN	Benign	0.90
PhyloP100		-0.59

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3131691;

hg19: chr1-40357268;

COSMIC: COSV68345121;