2-11349405-A-G

Variant names:

• chr2-11349405-A-G
• rs7581184
• ENST00000815406.1:n.*117A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000815406.1(ENSG00000306117):​n.*117A>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 152,076 control chromosomes in the GnomAD database, including 11,140 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.38 (11140 hom., cov: 33)
• Consequence: ENSG00000306117 ENST00000815406.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.447
• Publications: 7 publications found

Genes affected

ENSG00000306117 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000815406.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306117	ENST00000815406.1		n.*117A>G		downstream_gene	N/A
	ENSG00000306117	ENST00000815407.1		n.*117A>G		downstream_gene	N/A
	ENSG00000306117	ENST00000815408.1		n.*117A>G		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57705 AN: 151958 Hom.: 11133 Cov.: 33

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.380 AC: 57742 AN: 152076 Hom.: 11140 Cov.: 33 AF XY: 0.382 AC XY: 28405 AN XY: 74328

African (AFR) AF: 0.355 AC: 14739 AN: 41484

American (AMR) AF: 0.280 AC: 4282 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 1779 AN: 3472

East Asian (EAS) AF: 0.435 AC: 2255 AN: 5180

South Asian (SAS) AF: 0.377 AC: 1816 AN: 4816

European-Finnish (FIN) AF: 0.483 AC: 5104 AN: 10566

Middle Eastern (MID) AF: 0.353 AC: 103 AN: 292

European-Non Finnish (NFE) AF: 0.390 AC: 26478 AN: 67970

Other (OTH) AF: 0.396 AC: 833 AN: 2102

Alfa AF: 0.379 Hom.: 39522

Bravo AF: 0.365

Asia WGS AF: 0.416 AC: 1445 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	12
DANN	Benign	0.59
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs7581184; hg19: chr2-11489531;