chr6-32700073-C-G

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).

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

⚠️ 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 v4.3

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;