rs2001099

chr6-32415856-G-C

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 0.129 in 152,078 control chromosomes in the GnomAD database, including 1,547 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 0.13 (1547 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.171 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: 0.129 AC: 19565 AN: 151960 Hom.: 1547 Cov.: 31

Gnomad AFR AF: 0.0664

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.0904

Gnomad EAS AF: 0.0394

Gnomad SAS AF: 0.0473

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.129 AC: 19573 AN: 152078 Hom.: 1547 Cov.: 31 AF XY: 0.126 AC XY: 9354 AN XY: 74328

Gnomad4 AFR AF: 0.0666

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.0904

Gnomad4 EAS AF: 0.0392

Gnomad4 SAS AF: 0.0467

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.173

Gnomad4 OTH AF: 0.125

Alfa AF: 0.152 Hom.: 259

Bravo AF: 0.120

Asia WGS AF: 0.0580 AC: 203 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	7.9
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2001099; hg19: chr6-32383633;