rs525202

Variant names:

• chr11-34800401-A-C
• rs525202
• ENST00000843048.1:n.656+45794A>C

Your query was ambiguous. Multiple possible variants found:

• chr11-34800401-A-C
• chr11-34800401-A-G
• chr11-34800401-A-T

Variant summary

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

The ENST00000843048.1(ENSG00000309692):​n.656+45794A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.64 in 151,958 control chromosomes in the GnomAD database, including 31,906 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 0.64 (31906 hom., cov: 31)
• Consequence: ENSG00000309692 ENST00000843048.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.327
• Publications: 9 publications found

Genes affected

ENSG00000309692 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000843048.1. 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
	ENSG00000309692	ENST00000843048.1		n.656+45794A>C		intron	N/A
	ENSG00000309692	ENST00000843049.1		n.848+45794A>C		intron	N/A
	ENSG00000309692	ENST00000843050.1		n.440+45794A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.641 AC: 97284 AN: 151838 Hom.: 31909 Cov.: 31

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.658

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.764

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.704

Gnomad MID AF: 0.675

Gnomad NFE AF: 0.707

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.640 AC: 97312 AN: 151958 Hom.: 31906 Cov.: 31 AF XY: 0.640 AC XY: 47509 AN XY: 74284

African (AFR) AF: 0.505 AC: 20895 AN: 41408

American (AMR) AF: 0.631 AC: 9633 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.689 AC: 2391 AN: 3468

East Asian (EAS) AF: 0.764 AC: 3946 AN: 5166

South Asian (SAS) AF: 0.590 AC: 2835 AN: 4802

European-Finnish (FIN) AF: 0.704 AC: 7442 AN: 10570

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.707 AC: 48031 AN: 67970

Other (OTH) AF: 0.635 AC: 1340 AN: 2110

Alfa AF: 0.684 Hom.: 146286

Bravo AF: 0.632

Asia WGS AF: 0.636 AC: 2210 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.0
DANN	Benign	0.65
PhyloP100		0.33

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: rs525202;

hg19: chr11-34821948;