rs9275356

Variant names:

• chr6-32700073-C-G
• rs9275356

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM2 BP4_Strong BS1

The variant allele was found at a frequency of 0.0117 in 128,616 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.012 (0 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.656

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS1: Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0117 (1509/128616) while in subpopulation AMR AF= 0.0244 (265/10850). AF 95% confidence interval is 0.022. There are 0 homozygotes in gnomad4. There are 752 alleles in male gnomad4 subpopulation. Median coverage is 29. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0117 AC: 1506 AN: 128532 Hom.: 0 Cov.: 29

Gnomad AFR AF: 0.00533

Gnomad AMI AF: 0.0225

Gnomad AMR AF: 0.0244

Gnomad ASJ AF: 0.0245

Gnomad EAS AF: 0.00314

Gnomad SAS AF: 0.00448

Gnomad FIN AF: 0.0211

Gnomad MID AF: 0.00752

Gnomad NFE AF: 0.0128

Gnomad OTH AF: 0.00862

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

GnomAD4 genome AF: 0.0117 AC: 1509 AN: 128616 Hom.: 0 Cov.: 29 AF XY: 0.0120 AC XY: 752 AN XY: 62616

Gnomad4 AFR AF: 0.00534

Gnomad4 AMR AF: 0.0244

Gnomad4 ASJ AF: 0.0245

Gnomad4 EAS AF: 0.00315

Gnomad4 SAS AF: 0.00471

Gnomad4 FIN AF: 0.0211

Gnomad4 NFE AF: 0.0129

Gnomad4 OTH AF: 0.00851

Alfa AF: 0.0972 Hom.: 64

Bravo AF: 0.0988

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.9
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: rs9275356; hg19: chr6-32667850;