rs9268542

chr6-32416944-A-G

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 0.353 in 152,062 control chromosomes in the GnomAD database, including 10,105 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 0.35 (10105 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0970

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.485 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: 0.353 AC: 53643 AN: 151942 Hom.: 10098 Cov.: 32

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.353 AC: 53664 AN: 152062 Hom.: 10105 Cov.: 32 AF XY: 0.356 AC XY: 26479 AN XY: 74320

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.430

Gnomad4 ASJ AF: 0.537

Gnomad4 EAS AF: 0.474

Gnomad4 SAS AF: 0.501

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.368

Alfa AF: 0.392 Hom.: 17769

Bravo AF: 0.357

Asia WGS AF: 0.436 AC: 1511 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	5.5
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9268542; hg19: chr6-32384721;