chr2-175815518-C-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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000685522.2. 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
	ENSG00000289349	ENST00000685522.2		n.464-17093C>T		intron	N/A
	ENSG00000289349	ENST00000692740.2		n.326-17093C>T		intron	N/A
	ENSG00000289349	ENST00000840653.1		n.272-17093C>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11896469;

hg19: chr2-176680246;