rs10120023

Variant names:

• chr9-134918413-C-T
• rs10120023

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The variant allele was found at a frequency of 0.274 in 152,120 control chromosomes in the GnomAD database, including 6,228 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.27 (6228 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -4.28
• Publications: 38 publications found

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BP6: Variant 9-134918413-C-T is Benign according to our data. Variant chr9-134918413-C-T is described in ClinVar as Benign. ClinVar VariationId is 1266029.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41637 AN: 152002 Hom.: 6230 Cov.: 33

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.275

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.274 AC: 41625 AN: 152120 Hom.: 6228 Cov.: 33 AF XY: 0.272 AC XY: 20252 AN XY: 74344

African (AFR) AF: 0.163 AC: 6784 AN: 41516

American (AMR) AF: 0.234 AC: 3573 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1148 AN: 3470

East Asian (EAS) AF: 0.120 AC: 618 AN: 5166

South Asian (SAS) AF: 0.208 AC: 1001 AN: 4812

European-Finnish (FIN) AF: 0.371 AC: 3922 AN: 10566

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.345 AC: 23460 AN: 67988

Other (OTH) AF: 0.271 AC: 573 AN: 2114

Alfa AF: 0.317 Hom.: 14719

Bravo AF: 0.259

Asia WGS AF: 0.150 AC: 523 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Aug 22, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 22673311) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.079
DANN	Benign	0.47
PhyloP100		-4.3

Splicing

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

Other links and lift over

dbSNP: rs10120023; hg19: chr9-137810259;