rs35597309

chr6-32621489-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 0.0489 in 152,194 control chromosomes in the GnomAD database, including 224 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 0.049 (224 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.115 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: 0.0488 AC: 7418 AN: 152076 Hom.: 222 Cov.: 32

Gnomad AFR AF: 0.0704

Gnomad AMI AF: 0.0308

Gnomad AMR AF: 0.0390

Gnomad ASJ AF: 0.0360

Gnomad EAS AF: 0.0794

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0162

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0359

Gnomad OTH AF: 0.0554

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

GnomAD4 genome AF: 0.0489 AC: 7436 AN: 152194 Hom.: 224 Cov.: 32 AF XY: 0.0493 AC XY: 3666 AN XY: 74406

Gnomad4 AFR AF: 0.0706

Gnomad4 AMR AF: 0.0390

Gnomad4 ASJ AF: 0.0360

Gnomad4 EAS AF: 0.0790

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.0162

Gnomad4 NFE AF: 0.0359

Gnomad4 OTH AF: 0.0568

Alfa AF: 0.0408 Hom.: 20

Bravo AF: 0.0494

Asia WGS AF: 0.106 AC: 373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	6.9
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35597309; hg19: chr6-32589266;