rs13207034

Positions:

• chr6-92487582-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 0.0728 in 152,188 control chromosomes in the GnomAD database, including 733 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 0.073 (733 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0727 AC: 11056 AN: 152070 Hom.: 725 Cov.: 32

Gnomad AFR AF: 0.0156

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.0429

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0251

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0707

Gnomad OTH AF: 0.0811

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

GnomAD4 genome AF: 0.0728 AC: 11085 AN: 152188 Hom.: 733 Cov.: 32 AF XY: 0.0751 AC XY: 5586 AN XY: 74388

Gnomad4 AFR AF: 0.0156

Gnomad4 AMR AF: 0.187

Gnomad4 ASJ AF: 0.0429

Gnomad4 EAS AF: 0.285

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.0251

Gnomad4 NFE AF: 0.0707

Gnomad4 OTH AF: 0.0878

Alfa AF: 0.0640 Hom.: 66

Bravo AF: 0.0839

Asia WGS AF: 0.192 AC: 669 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.2
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13207034; hg19: chr6-93197300;