rs3759843

Positions:

• chr15-40160874-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 0.153 in 299,910 control chromosomes in the GnomAD database, including 4,296 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.15 (1983 hom., cov: 33)
  • Exomes 𝑓: 0.16 (2313 hom.)
• Consequence: intergenic_region
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -2.67

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BP6: Variant 15-40160874-G-A is Benign according to our data. Variant chr15-40160874-G-A is described in ClinVar as [Benign]. Clinvar id is 1289187.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.40160874G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22538 AN: 152152 Hom.: 1984 Cov.: 33

Gnomad AFR AF: 0.0775

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.00442

Gnomad SAS AF: 0.0689

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.128

GnomAD4 exome AF: 0.158 AC: 23301 AN: 147640 Hom.: 2313 AF XY: 0.156 AC XY: 11487 AN XY: 73528

Gnomad4 AFR exome AF: 0.0764

Gnomad4 AMR exome AF: 0.0939

Gnomad4 ASJ exome AF: 0.198

Gnomad4 EAS exome AF: 0.00428

Gnomad4 SAS exome AF: 0.0596

Gnomad4 FIN exome AF: 0.223

Gnomad4 NFE exome AF: 0.190

Gnomad4 OTH exome AF: 0.163

GnomAD4 genome AF: 0.148 AC: 22533 AN: 152270 Hom.: 1983 Cov.: 33 AF XY: 0.146 AC XY: 10880 AN XY: 74452

Gnomad4 AFR AF: 0.0773

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.00424

Gnomad4 SAS AF: 0.0684

Gnomad4 FIN AF: 0.241

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.127

Alfa AF: 0.156 Hom.: 421

Bravo AF: 0.137

Asia WGS AF: 0.0440 AC: 152 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	Jan 10, 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	-0.95
CADD	Benign	0.25
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3759843; hg19: chr15-40453075;