rs11103377

Positions:

• chr9-136205289-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 0.461 in 151,630 control chromosomes in the GnomAD database, including 16,613 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.46 (16613 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.80

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP6: Variant 9-136205289-A-G is Benign according to our data. Variant chr9-136205289-A-G is described in ClinVar as [Benign]. Clinvar id is 1288710.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.525 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: 0.461 AC: 69829 AN: 151514 Hom.: 16613 Cov.: 31

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.461 AC: 69843 AN: 151630 Hom.: 16613 Cov.: 31 AF XY: 0.456 AC XY: 33787 AN XY: 74114

Gnomad4 AFR AF: 0.380

Gnomad4 AMR AF: 0.427

Gnomad4 ASJ AF: 0.464

Gnomad4 EAS AF: 0.356

Gnomad4 SAS AF: 0.420

Gnomad4 FIN AF: 0.435

Gnomad4 NFE AF: 0.530

Gnomad4 OTH AF: 0.472

Alfa AF: 0.483 Hom.: 2238

Bravo AF: 0.456

Asia WGS AF: 0.382 AC: 1326 AN: 3476

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

Jun 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.0
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11103377; hg19: chr9-139097135;