rs13192563

Positions:

• chr6-52200438-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.249

Gnomad4 AMR AF: 0.729

Gnomad4 ASJ AF: 0.614

Gnomad4 EAS AF: 0.689

Gnomad4 SAS AF: 0.647

Gnomad4 FIN AF: 0.771

Gnomad4 NFE AF: 0.757

Gnomad4 OTH AF: 0.636

Alfa AF: 0.665 Hom.: 4407

Bravo AF: 0.588

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13192563; hg19: chr6-52065236;