9-35658075-A-G

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 0.315 in 615,678 control chromosomes in the GnomAD database, including 32,828 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.27 (6164 hom., cov: 33)
  • Exomes 𝑓: 0.33 (26664 hom.)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -3.88

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BP6: Variant 9-35658075-A-G is Benign according to our data. Variant chr9-35658075-A-G is described in ClinVar as [Benign]. Clinvar id is 138920.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.468 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: 0.266 AC: 40452 AN: 151924 Hom.: 6164 Cov.: 33

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.266

GnomAD4 exome AF: 0.331 AC: 153551 AN: 463636 Hom.: 26664 Cov.: 0 AF XY: 0.334 AC XY: 81874 AN XY: 244998

Gnomad4 AFR exome AF: 0.117

Gnomad4 AMR exome AF: 0.344

Gnomad4 ASJ exome AF: 0.336

Gnomad4 EAS exome AF: 0.529

Gnomad4 SAS exome AF: 0.375

Gnomad4 FIN exome AF: 0.340

Gnomad4 NFE exome AF: 0.310

Gnomad4 OTH exome AF: 0.323

GnomAD4 genome AF: 0.266 AC: 40445 AN: 152042 Hom.: 6164 Cov.: 33 AF XY: 0.271 AC XY: 20122 AN XY: 74316

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.337

Gnomad4 EAS AF: 0.484

Gnomad4 SAS AF: 0.371

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.264

Alfa AF: 0.144 Hom.: 265

Bravo AF: 0.259

Asia WGS AF: 0.412 AC: 1430 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Anauxetic dysplasia Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	0.0010
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3829077; hg19: chr9-35658072;