rs13192563

Variant names:

• chr6-52200438-G-A
• rs13192563

Variant summary

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

The variant allele was found at a frequency of 0.606 in 151,736 control chromosomes in the GnomAD database, including 31,631 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 0.61 (31631 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.751 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.606 AC: 91869 AN: 151618 Hom.: 31623 Cov.: 32

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.771

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.757

Gnomad OTH AF: 0.634

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

GnomAD4 genome AF: 0.606 AC: 91890 AN: 151736 Hom.: 31631 Cov.: 32 AF XY: 0.608 AC XY: 45111 AN XY: 74150

African (AFR) AF: 0.249 AC: 10301 AN: 41386

American (AMR) AF: 0.729 AC: 11111 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2132 AN: 3470

East Asian (EAS) AF: 0.689 AC: 3554 AN: 5156

South Asian (SAS) AF: 0.647 AC: 3117 AN: 4814

European-Finnish (FIN) AF: 0.771 AC: 8114 AN: 10528

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

European-Non Finnish (NFE) AF: 0.757 AC: 51318 AN: 67830

Other (OTH) AF: 0.636 AC: 1337 AN: 2102

Alfa AF: 0.648 Hom.: 4426

Bravo AF: 0.588

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.6
DANN	Benign	0.83
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs13192563; hg19: chr6-52065236;