chr2-9557042-A-G

Variant names:

• chr2-9557042-A-G
• rs11684747
• ENST00000607241.2:n.1169A>G

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The ENST00000607241.2(ENSG00000271855):​n.1169A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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: ENSG00000271855 ENST00000607241.2 non_coding_transcript_exon
• Clinical Significance: Likely benign no assertion criteria provided B:1
• Conservation: PhyloP100: -0.107
• Publications: 24 publications found

Genes affected

ENSG00000271855 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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
ENSG00000271855	ENST00000607241.2	n.1169A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000271855	ENST00000716659.1	n.307+450A>G		intron_variant	Intron 1 of 2
ENSG00000271855	ENST00000716660.1	n.278+450A>G		intron_variant	Intron 1 of 2
ENSG00000271855	ENST00000830797.1	n.251+450A>G		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.191 AC: 7926 AN: 41500

American (AMR) AF: 0.154 AC: 2352 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 827 AN: 3468

East Asian (EAS) AF: 0.0249 AC: 129 AN: 5184

South Asian (SAS) AF: 0.0962 AC: 464 AN: 4822

European-Finnish (FIN) AF: 0.151 AC: 1600 AN: 10572

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 14005 AN: 67984

Other (OTH) AF: 0.204 AC: 431 AN: 2112

Alfa AF: 0.205 Hom.: 4085

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
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs11684747; hg19: chr2-9697171;