rs11684747

Variant names:

• chr2-9557042-A-G
• rs11684747

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The variant allele was found at a frequency of 0.185 in 152,122 control chromosomes in the GnomAD database, including 2,746 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

• Frequency: Genomes: 𝑓 0.19 (2746 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Likely benign no assertion criteria provided B:1
• Conservation: PhyloP100: -0.107

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 2-9557042-A-G is Benign according to our data. Variant chr2-9557042-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 3235267.Status of the report is no_assertion_criteria_provided, 0 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.203 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: 0.185 AC: 28148 AN: 152004 Hom.: 2742 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.0250

Gnomad SAS AF: 0.0964

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.185 AC: 28173 AN: 152122 Hom.: 2746 Cov.: 32 AF XY: 0.181 AC XY: 13445 AN XY: 74386

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.238

Gnomad4 EAS AF: 0.0249

Gnomad4 SAS AF: 0.0962

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.204

Alfa AF: 0.205 Hom.: 3161

Bravo AF: 0.190

Asia WGS AF: 0.0920 AC: 322 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

Mycobacterium tuberculosis, susceptibility to Benign:1

Dec 21, 2023

Laboratory Of Immunobiology And Genetics, Instituto Nacional De Enfermedades Respiratorias Ismael Cosio Villegas

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: research

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.1
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: rs11684747; hg19: chr2-9697171;