chr1-39883663-C-CT

Position:

• chr1-39883663-C-CT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NR_183424.1(MYCL-AS1):​n.272+255dup variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0793 in 146,096 control chromosomes in the GnomAD database, including 577 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.079 (577 hom., cov: 30)
• Consequence: MYCL-AS1 NR_183424.1 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.796

Genes affected

MYCL-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 1-39883663-C-CT is Benign according to our data. Variant chr1-39883663-C-CT is described in ClinVar as [Benign]. Clinvar id is 1276471.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYCL-AS1	NR_183424.1	n.272+255dup		intron_variant, non_coding_transcript_variant
MYCL-AS1	NR_183425.1	n.35+492dup		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0793 AC: 11581 AN: 146060 Hom.: 577 Cov.: 30

Gnomad AFR AF: 0.0234

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.0957

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.00119

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0913

Gnomad MID AF: 0.0828

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0770

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

GnomAD4 genome AF: 0.0793 AC: 11579 AN: 146096 Hom.: 577 Cov.: 30 AF XY: 0.0777 AC XY: 5518 AN XY: 71038

Gnomad4 AFR AF: 0.0233

Gnomad4 AMR AF: 0.0957

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.00119

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.0913

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.0770

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 06, 2019

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs58870544; hg19: chr1-40349335;