2-110691564-A-G

Variant names:

• chr2-110691564-A-G
• rs11694702
• ENST00000703531.1:n.373+12967A>G

Variant summary

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

The ENST00000703531.1(ENSG00000289202):​n.373+12967A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.838 in 152,208 control chromosomes in the GnomAD database, including 53,797 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 0.84 (53797 hom., cov: 32)
• Consequence: ENSG00000289202 ENST00000703531.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.420
• Publications: 7 publications found

Genes affected

ENSG00000289202 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.94 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000703531.1. 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
	ENSG00000289202	ENST00000703531.1		n.373+12967A>G		intron	N/A
	ENSG00000289202	ENST00000722170.1		n.391-955A>G		intron	N/A
	ENSG00000289202	ENST00000722171.1		n.137-955A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.838 AC: 127394 AN: 152090 Hom.: 53743 Cov.: 32

Gnomad AFR AF: 0.947

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.872

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.767

Gnomad FIN AF: 0.817

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.789

Gnomad OTH AF: 0.805

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

GnomAD4 genome AF: 0.838 AC: 127510 AN: 152208 Hom.: 53797 Cov.: 32 AF XY: 0.838 AC XY: 62358 AN XY: 74382

African (AFR) AF: 0.947 AC: 39362 AN: 41548

American (AMR) AF: 0.873 AC: 13345 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.719 AC: 2496 AN: 3472

East Asian (EAS) AF: 0.728 AC: 3759 AN: 5164

South Asian (SAS) AF: 0.767 AC: 3693 AN: 4818

European-Finnish (FIN) AF: 0.817 AC: 8650 AN: 10588

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.789 AC: 53638 AN: 68004

Other (OTH) AF: 0.805 AC: 1701 AN: 2114

Alfa AF: 0.806 Hom.: 122596

Bravo AF: 0.846

Asia WGS AF: 0.764 AC: 2656 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.65
PhyloP100		-0.42

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: rs11694702;

hg19: chr2-111449141;