rs3916027

Positions:

• chr8-19967357-G-A
• chr8-19967357-G-T

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 0.303 in 152,084 control chromosomes in the GnomAD database, including 7,353 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.30 (7351 hom., cov: 33)
  • Exomes 𝑓: 0.23 (2 hom.)
• Consequence: intergenic_region
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.0550

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BP6: Variant 8-19967357-G-A is Benign according to our data. Variant chr8-19967357-G-A is described in ClinVar as [Benign]. Clinvar id is 1227639.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.399 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.19967357G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.303 AC: 46008 AN: 151902 Hom.: 7340 Cov.: 33

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.290

GnomAD4 exome AF: 0.234 AC: 15 AN: 64 Hom.: 2 AF XY: 0.229 AC XY: 11 AN XY: 48

Gnomad4 FIN exome AF: 0.226

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.303 AC: 46042 AN: 152020 Hom.: 7351 Cov.: 33 AF XY: 0.300 AC XY: 22276 AN XY: 74302

Gnomad4 AFR AF: 0.404

Gnomad4 AMR AF: 0.262

Gnomad4 ASJ AF: 0.371

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.291

Alfa AF: 0.303 Hom.: 1353

Bravo AF: 0.308

Asia WGS AF: 0.242 AC: 839 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	Apr 14, 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	-0.97
CADD	Benign	2.1
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3916027; hg19: chr8-19824868;