rs9275356

Variant names:

• chr6-32700073-C-G
• rs9275356

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

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
• Publications: 9 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Variant has high frequency in the AMR (0.022) population. However there is too low homozygotes in high coverage region: (expected more than 4, got 0).
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00534 AC: 207 AN: 38760

American (AMR) AF: 0.0244 AC: 265 AN: 10850

Ashkenazi Jewish (ASJ) AF: 0.0245 AC: 62 AN: 2532

East Asian (EAS) AF: 0.00315 AC: 14 AN: 4446

South Asian (SAS) AF: 0.00471 AC: 20 AN: 4242

European-Finnish (FIN) AF: 0.0211 AC: 182 AN: 8634

Middle Eastern (MID) AF: 0.00806 AC: 2 AN: 248

European-Non Finnish (NFE) AF: 0.0129 AC: 726 AN: 56432

Other (OTH) AF: 0.00851 AC: 15 AN: 1762

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.0972 Hom.: 64

Bravo AF: 0.0988

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.9
DANN	Benign	0.51
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs9275356; hg19: chr6-32667850;