9-35658073-T-C

Position:

• chr9-35658073-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 0.135 in 613,924 control chromosomes in the GnomAD database, including 6,974 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.17 (2806 hom., cov: 34)
  • Exomes 𝑓: 0.12 (4168 hom.)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:2
• Conservation: PhyloP100: -6.17

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant 9-35658073-T-C is Benign according to our data. Variant chr9-35658073-T-C is described in ClinVar as [Benign]. Clinvar id is 138921.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.303 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: 26035 AN: 152034 Hom.: 2789 Cov.: 34

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.0700

Gnomad EAS AF: 0.0350

Gnomad SAS AF: 0.0892

Gnomad FIN AF: 0.0859

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.164

GnomAD4 exome AF: 0.123 AC: 57008 AN: 461772 Hom.: 4168 Cov.: 0 AF XY: 0.121 AC XY: 29672 AN XY: 244216

Gnomad4 AFR exome AF: 0.307

Gnomad4 AMR exome AF: 0.109

Gnomad4 ASJ exome AF: 0.0742

Gnomad4 EAS exome AF: 0.0255

Gnomad4 SAS exome AF: 0.0941

Gnomad4 FIN exome AF: 0.0892

Gnomad4 NFE exome AF: 0.138

Gnomad4 OTH exome AF: 0.130

GnomAD4 genome AF: 0.172 AC: 26099 AN: 152152 Hom.: 2806 Cov.: 34 AF XY: 0.165 AC XY: 12288 AN XY: 74398

Gnomad4 AFR AF: 0.308

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.0700

Gnomad4 EAS AF: 0.0351

Gnomad4 SAS AF: 0.0893

Gnomad4 FIN AF: 0.0859

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.165

Alfa AF: 0.0677 Hom.: 76

Bravo AF: 0.182

Asia WGS AF: 0.0930 AC: 324 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, single submitter

Submissions by phenotype

Metaphyseal chondrodysplasia, McKusick type Benign:1

Benign, no assertion criteria provided

clinical testing

Natera, Inc.

Sep 16, 2020

- -

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	-0.82
CADD	Benign	0.0010
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12551232; hg19: chr9-35658070;