ENST00000685522.2:n.464-17093C>T

Variant names:

• chr2-175815518-C-T
• rs11896469
• ENST00000685522.2:n.464-17093C>T

Variant summary

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

The ENST00000685522.2(ENSG00000289349):​n.464-17093C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.664 in 152,082 control chromosomes in the GnomAD database, including 35,064 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 0.66 (35064 hom., cov: 32)
• Consequence: ENSG00000289349 ENST00000685522.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.70
• Publications: 6 publications found

Genes affected

ENSG00000289349 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985962	XR_007087312.1	n.149+23372G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289349	ENST00000685522.2	n.464-17093C>T		intron_variant	Intron 1 of 2
ENSG00000289349	ENST00000692740.2	n.326-17093C>T		intron_variant	Intron 2 of 3
ENSG00000289349	ENST00000840653.1	n.272-17093C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.664 AC: 100904 AN: 151964 Hom.: 35002 Cov.: 32

Gnomad AFR AF: 0.876

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.657

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

GnomAD4 genome AF: 0.664 AC: 101025 AN: 152082 Hom.: 35064 Cov.: 32 AF XY: 0.667 AC XY: 49584 AN XY: 74342

African (AFR) AF: 0.876 AC: 36352 AN: 41506

American (AMR) AF: 0.628 AC: 9601 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.564 AC: 1957 AN: 3472

East Asian (EAS) AF: 0.585 AC: 3020 AN: 5158

South Asian (SAS) AF: 0.688 AC: 3307 AN: 4806

European-Finnish (FIN) AF: 0.617 AC: 6533 AN: 10580

Middle Eastern (MID) AF: 0.538 AC: 157 AN: 292

European-Non Finnish (NFE) AF: 0.566 AC: 38435 AN: 67960

Other (OTH) AF: 0.656 AC: 1384 AN: 2110

Alfa AF: 0.596 Hom.: 109428

Bravo AF: 0.670

Asia WGS AF: 0.698 AC: 2427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.23
DANN	Benign	0.51
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs11896469; hg19: chr2-176680246;