1-39883738-T-C

Position:

• chr1-39883738-T-C

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 0.566 in 151,554 control chromosomes in the GnomAD database, including 26,451 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency: Genomes: 𝑓 0.57 (26451 hom., cov: 29)
• Consequence: intergenic_region
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -1.33

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant 1-39883738-T-C is Benign according to our data. Variant chr1-39883738-T-C is described in ClinVar as [Benign]. Clinvar id is 1274712.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.39883738T>C		intergenic_region
MYCL-AS1	NR_183424.1	n.272+317T>C		intron_variant
MYCL-AS1	NR_183425.1	n.35+554T>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.566 AC: 85742 AN: 151436 Hom.: 26394 Cov.: 29

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.524

Gnomad EAS AF: 0.598

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.566 AC: 85850 AN: 151554 Hom.: 26451 Cov.: 29 AF XY: 0.564 AC XY: 41735 AN XY: 74042

Gnomad4 AFR AF: 0.830

Gnomad4 AMR AF: 0.488

Gnomad4 ASJ AF: 0.524

Gnomad4 EAS AF: 0.598

Gnomad4 SAS AF: 0.479

Gnomad4 FIN AF: 0.469

Gnomad4 NFE AF: 0.451

Gnomad4 OTH AF: 0.513

Alfa AF: 0.509 Hom.: 2494

Bravo AF: 0.581

Asia WGS AF: 0.587 AC: 2039 AN: 3476

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	-0.89
CADD	Benign	4.5
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7535397; hg19: chr1-40349410;