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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370120	XR_007063725.1	n.618A>G		non_coding_transcript_exon_variant	Exon 2 of 2
LOC105370120	XR_007063726.1	n.341A>G		non_coding_transcript_exon_variant	Exon 3 of 3
LOC105370120	XR_007063727.1	n.1220A>G		non_coding_transcript_exon_variant	Exon 2 of 2
LOC105370120	XR_007063728.1	n.335A>G		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305468	ENST00000811169.1	n.692A>G		non_coding_transcript_exon_variant	Exon 4 of 4
ENSG00000305468	ENST00000811172.1	n.938A>G		non_coding_transcript_exon_variant	Exon 4 of 4
ENSG00000305468	ENST00000811173.1	n.989A>G		non_coding_transcript_exon_variant	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 v4.3

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

Other links and lift over

dbSNP: rs2994906; hg19: chr13-25693092;