rs17838831

Positions:

• chr3-149222074-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 0.162 in 370,016 control chromosomes in the GnomAD database, including 5,416 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.16 (2158 hom., cov: 32)
  • Exomes 𝑓: 0.16 (3258 hom.)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -1.03

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant 3-149222074-T-C is Benign according to our data. Variant chr3-149222074-T-C is described in ClinVar as [Benign]. Clinvar id is 1293787.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24882 AN: 152058 Hom.: 2151 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.0960

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.167

GnomAD3 exomes AF: 0.180 AC: 8277 AN: 45908 Hom.: 930 AF XY: 0.182 AC XY: 4275 AN XY: 23530

Gnomad AFR exome AF: 0.155

Gnomad AMR exome AF: 0.190

Gnomad ASJ exome AF: 0.0850

Gnomad EAS exome AF: 0.321

Gnomad SAS exome AF: 0.200

Gnomad FIN exome AF: 0.184

Gnomad NFE exome AF: 0.139

Gnomad OTH exome AF: 0.166

GnomAD4 exome AF: 0.161 AC: 35099 AN: 217840 Hom.: 3258 Cov.: 0 AF XY: 0.163 AC XY: 19014 AN XY: 116342

Gnomad4 AFR exome AF: 0.153

Gnomad4 AMR exome AF: 0.196

Gnomad4 ASJ exome AF: 0.0997

Gnomad4 EAS exome AF: 0.319

Gnomad4 SAS exome AF: 0.188

Gnomad4 FIN exome AF: 0.180

Gnomad4 NFE exome AF: 0.140

Gnomad4 OTH exome AF: 0.164

GnomAD4 genome AF: 0.164 AC: 24915 AN: 152176 Hom.: 2158 Cov.: 32 AF XY: 0.167 AC XY: 12404 AN XY: 74394

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.183

Gnomad4 ASJ AF: 0.0960

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.169

Alfa AF: 0.144 Hom.: 1706

Bravo AF: 0.165

Asia WGS AF: 0.258 AC: 896 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	Jul 09, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.0
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17838831; hg19: chr3-148939861;