rs1799729

chr9-34637993-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The variant allele was found at a frequency of 0.162 in 401,558 control chromosomes in the GnomAD database, including 5,709 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.17 (2248 hom., cov: 33)
  • Exomes 𝑓: 0.16 (3461 hom.)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0170

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BP6: Variant 9-34637993-G-A is Benign according to our data. Variant chr9-34637993-G-A is described in ClinVar as [Benign]. Clinvar id is 1271335.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.296 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: 0.171 AC: 25977 AN: 152132 Hom.: 2249 Cov.: 33

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.184

GnomAD4 exome AF: 0.157 AC: 39161 AN: 249308 Hom.: 3461 AF XY: 0.156 AC XY: 19808 AN XY: 127084

Gnomad4 AFR exome AF: 0.155

Gnomad4 AMR exome AF: 0.231

Gnomad4 ASJ exome AF: 0.129

Gnomad4 EAS exome AF: 0.295

Gnomad4 SAS exome AF: 0.142

Gnomad4 FIN exome AF: 0.109

Gnomad4 NFE exome AF: 0.148

Gnomad4 OTH exome AF: 0.156

GnomAD4 genome AF: 0.171 AC: 25977 AN: 152250 Hom.: 2248 Cov.: 33 AF XY: 0.171 AC XY: 12707 AN XY: 74446

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.308

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.181

Alfa AF: 0.162 Hom.: 388

Bravo AF: 0.181

Asia WGS AF: 0.252 AC: 878 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 03, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	3.7
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1799729; hg19: chr9-34637990; COSMIC: COSV52844869;