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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373554	XR_007087178.1	n.3799-955A>G		intron_variant	Intron 1 of 1
LOC105373554	XR_923189.4	n.387-955A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289202	ENST00000703531.1	n.373+12967A>G		intron_variant	Intron 1 of 4
ENSG00000289202	ENST00000722170.1	n.391-955A>G		intron_variant	Intron 1 of 1
ENSG00000289202	ENST00000722171.1	n.137-955A>G		intron_variant	Intron 1 of 1

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 v4.3

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

Other links and lift over

dbSNP: rs11694702; hg19: chr2-111449141;