rs2994906

Variant names:

• chr13-25118954-A-G
• rs2994906
• ENST00000811169.1:n.692A>G

Variant summary

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

The ENST00000811169.1(ENSG00000305468):​n.692A>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 0.798 in 151,774 control chromosomes in the GnomAD database, including 48,431 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 0.80 (48431 hom., cov: 28)
• Consequence: ENSG00000305468 ENST00000811169.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 2 publications found

Genes affected

ENSG00000305468 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000811169.1. 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
	ENSG00000305468	ENST00000811169.1		n.692A>G		non_coding_transcript_exon	Exon 4 of 4
	ENSG00000305468	ENST00000811172.1		n.938A>G		non_coding_transcript_exon	Exon 4 of 4
	ENSG00000305468	ENST00000811173.1		n.989A>G		non_coding_transcript_exon	Exon 5 of 5

Frequencies

GnomAD3 genomes AF: 0.798 AC: 121091 AN: 151656 Hom.: 48400 Cov.: 28

Gnomad AFR AF: 0.797

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.867

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.801

Gnomad SAS AF: 0.877

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.815

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

GnomAD4 genome AF: 0.798 AC: 121177 AN: 151774 Hom.: 48431 Cov.: 28 AF XY: 0.801 AC XY: 59474 AN XY: 74204

African (AFR) AF: 0.797 AC: 32936 AN: 41350

American (AMR) AF: 0.867 AC: 13246 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.810 AC: 2806 AN: 3464

East Asian (EAS) AF: 0.801 AC: 4120 AN: 5146

South Asian (SAS) AF: 0.877 AC: 4182 AN: 4768

European-Finnish (FIN) AF: 0.772 AC: 8147 AN: 10554

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.783 AC: 53178 AN: 67910

Other (OTH) AF: 0.810 AC: 1705 AN: 2104

Alfa AF: 0.787 Hom.: 11703

Bravo AF: 0.806

Asia WGS AF: 0.833 AC: 2897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.0030
DANN	Benign	0.19
PhyloP100		-1.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2994906;

hg19: chr13-25693092;