rs34387655

Variant names:

• chr1-39891568-A-C
• rs34387655
• ENST00000418255.2:n.326-6175A>C

Variant summary

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

The ENST00000418255.2(MYCL-AS1):​n.326-6175A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.096 in 152,092 control chromosomes in the GnomAD database, including 1,096 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 0.096 (1096 hom., cov: 32)
• Consequence: MYCL-AS1 ENST00000418255.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19
• Publications: 4 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYCL-AS1	NR_183424.1	n.273-6175A>C		intron_variant	Intron 1 of 2
MYCL-AS1	NR_183425.1	n.36-6175A>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYCL-AS1	ENST00000418255.2	n.326-6175A>C		intron_variant	Intron 1 of 2	2
MYCL-AS1	ENST00000837551.1	n.304-6175A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0959 AC: 14572 AN: 151974 Hom.: 1089 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0519

Gnomad ASJ AF: 0.0490

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0242

Gnomad FIN AF: 0.0740

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0578

Gnomad OTH AF: 0.0916

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

GnomAD4 genome AF: 0.0960 AC: 14599 AN: 152092 Hom.: 1096 Cov.: 32 AF XY: 0.0946 AC XY: 7036 AN XY: 74362

African (AFR) AF: 0.206 AC: 8547 AN: 41456

American (AMR) AF: 0.0518 AC: 792 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0490 AC: 170 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5180

South Asian (SAS) AF: 0.0249 AC: 120 AN: 4824

European-Finnish (FIN) AF: 0.0740 AC: 783 AN: 10584

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0578 AC: 3929 AN: 67980

Other (OTH) AF: 0.0906 AC: 191 AN: 2108

Alfa AF: 0.104 Hom.: 187

Bravo AF: 0.0999

Asia WGS AF: 0.0280 AC: 100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	9.3
DANN	Benign	0.65
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs34387655; hg19: chr1-40357240;