rs11689287

Variant names:

• chr2-127130761-T-C
• rs11689287
• ENST00000726607.1:n.342-4499T>C

Variant summary

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

The ENST00000726607.1(ENSG00000294899):​n.342-4499T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 150,540 control chromosomes in the GnomAD database, including 1,355 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 0.13 (1355 hom., cov: 30)
• Consequence: ENSG00000294899 ENST00000726607.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96
• Publications: 1 publications found

Genes affected

ENSG00000294899 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373605	XR_923310.3	n.449-2477T>C		intron_variant	Intron 2 of 3
LOC105373605	XR_923311.4	n.846-2477T>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294899	ENST00000726607.1	n.342-4499T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19360 AN: 150434 Hom.: 1352 Cov.: 30

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.0586

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.0114

Gnomad SAS AF: 0.0732

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.129 AC: 19375 AN: 150540 Hom.: 1355 Cov.: 30 AF XY: 0.125 AC XY: 9225 AN XY: 73518

African (AFR) AF: 0.119 AC: 4841 AN: 40820

American (AMR) AF: 0.100 AC: 1519 AN: 15116

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 439 AN: 3456

East Asian (EAS) AF: 0.0114 AC: 58 AN: 5072

South Asian (SAS) AF: 0.0727 AC: 348 AN: 4790

European-Finnish (FIN) AF: 0.143 AC: 1472 AN: 10260

Middle Eastern (MID) AF: 0.103 AC: 30 AN: 292

European-Non Finnish (NFE) AF: 0.153 AC: 10356 AN: 67742

Other (OTH) AF: 0.124 AC: 259 AN: 2088

Alfa AF: 0.150 Hom.: 176

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.052
DANN	Benign	0.31
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs11689287; hg19: chr2-127888337; COSMIC: COSV65787146;