rs9275698

chr6-32720196-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 0.369 in 149,858 control chromosomes in the GnomAD database, including 10,488 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 0.37 (10488 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.43 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: 0.369 AC: 55283 AN: 149738 Hom.: 10476 Cov.: 31

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.369 AC: 55330 AN: 149858 Hom.: 10488 Cov.: 31 AF XY: 0.365 AC XY: 26642 AN XY: 73022

Gnomad4 AFR AF: 0.435

Gnomad4 AMR AF: 0.355

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.276

Gnomad4 SAS AF: 0.424

Gnomad4 FIN AF: 0.242

Gnomad4 NFE AF: 0.353

Gnomad4 OTH AF: 0.418

Alfa AF: 0.348 Hom.: 13642

Bravo AF: 0.370

Asia WGS AF: 0.324 AC: 1127 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.71
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9275698; hg19: chr6-32687973;