chr1-39883661-G-A

Position:

• chr1-39883661-G-A

Variant summary

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

The variant allele was found at a frequency of 0.0515 in 515,662 control chromosomes in the GnomAD database, including 1,093 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.075 (545 hom., cov: 32)
  • Exomes 𝑓: 0.042 (548 hom.)
• Consequence: intergenic_region
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -1.07

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BP6: Variant 1-39883661-G-A is Benign according to our data. Variant chr1-39883661-G-A is described in ClinVar as [Benign]. Clinvar id is 1221668.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.39883661G>A		intergenic_region
MYCL-AS1	NR_183424.1	n.272+240G>A		intron_variant
MYCL-AS1	NR_183425.1	n.35+477G>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0746 AC: 11175 AN: 149788 Hom.: 543 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.0378

Gnomad AMR AF: 0.0451

Gnomad ASJ AF: 0.0504

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0238

Gnomad FIN AF: 0.0720

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0579

Gnomad OTH AF: 0.0732

GnomAD4 exome AF: 0.0420 AC: 15369 AN: 365764 Hom.: 548 AF XY: 0.0415 AC XY: 7856 AN XY: 189284

Gnomad4 AFR exome AF: 0.118

Gnomad4 AMR exome AF: 0.0319

Gnomad4 ASJ exome AF: 0.0480

Gnomad4 EAS exome AF: 0.0000428

Gnomad4 SAS exome AF: 0.0187

Gnomad4 FIN exome AF: 0.0605

Gnomad4 NFE exome AF: 0.0431

Gnomad4 OTH exome AF: 0.0488

GnomAD4 genome AF: 0.0746 AC: 11182 AN: 149898 Hom.: 545 Cov.: 32 AF XY: 0.0732 AC XY: 5356 AN XY: 73180

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.0450

Gnomad4 ASJ AF: 0.0504

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0245

Gnomad4 FIN AF: 0.0720

Gnomad4 NFE AF: 0.0579

Gnomad4 OTH AF: 0.0724

Alfa AF: 0.0735 Hom.: 58

Bravo AF: 0.0754

Asia WGS AF: 0.0230 AC: 80 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	clinical testing	GeneDx	Aug 13, 2019	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	3.4
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs61318917; hg19: chr1-40349333;