chr1-39883756-G-A

Position:

• chr1-39883756-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NR_183424.1(MYCL-AS1):​n.272+335G>A 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 0.187 in 151,176 control chromosomes in the GnomAD database, including 2,792 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency: Genomes: 𝑓 0.19 (2792 hom., cov: 32)
• Consequence: MYCL-AS1 NR_183424.1 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.277

Genes affected

MYCL-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BP6: Variant 1-39883756-G-A is Benign according to our data. Variant chr1-39883756-G-A is described in ClinVar as [Benign]. Clinvar id is 1289286.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYCL-AS1	NR_183424.1	n.272+335G>A		intron_variant, non_coding_transcript_variant
MYCL-AS1	NR_183425.1	n.35+572G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28330 AN: 151058 Hom.: 2791 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.0901

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.00987

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.187 AC: 28331 AN: 151176 Hom.: 2792 Cov.: 32 AF XY: 0.182 AC XY: 13422 AN XY: 73810

Gnomad4 AFR AF: 0.189

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.00989

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.217

Gnomad4 OTH AF: 0.160

Alfa AF: 0.0923 Hom.: 135

Bravo AF: 0.183

Asia WGS AF: 0.111 AC: 388 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 14, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	11
DANN	Uncertain	0.97

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs61781270; hg19: chr1-40349428;