rs9563646

Variant names:

• chr13-58760600-C-A
• rs9563646
• XR_941987.3:n.509-3389C>A

Your query was ambiguous. Multiple possible variants found:

• chr13-58760600-C-A
• chr13-58760600-C-G
• chr13-58760600-C-T

Variant summary

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

The XR_941987.3(LOC105370220):​n.509-3389C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.66 in 151,836 control chromosomes in the GnomAD database, including 33,275 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 (33275 hom., cov: 31)
• Consequence: LOC105370220 XR_941987.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970
• Publications: 2 publications found

Genes affected

LOC105370220 (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 = 0.793 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.660 AC: 100199 AN: 151718 Hom.: 33246 Cov.: 31

Gnomad AFR AF: 0.651

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.813

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.661

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

GnomAD4 genome AF: 0.660 AC: 100276 AN: 151836 Hom.: 33275 Cov.: 31 AF XY: 0.659 AC XY: 48896 AN XY: 74232

African (AFR) AF: 0.651 AC: 26979 AN: 41428

American (AMR) AF: 0.649 AC: 9898 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.661 AC: 2295 AN: 3470

East Asian (EAS) AF: 0.814 AC: 4199 AN: 5160

South Asian (SAS) AF: 0.698 AC: 3363 AN: 4820

European-Finnish (FIN) AF: 0.627 AC: 6595 AN: 10526

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.660 AC: 44759 AN: 67864

Other (OTH) AF: 0.662 AC: 1398 AN: 2112

Alfa AF: 0.657 Hom.: 48347

Bravo AF: 0.664

Asia WGS AF: 0.749 AC: 2600 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.70
DANN	Benign	0.65
PhyloP100		-0.097

Splicing

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

Other links and lift over

dbSNP: rs9563646; hg19: chr13-59334734;