rs9658056

Variant names:

• chr6-35341783-C-T
• rs9658056

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.028 in 150,990 control chromosomes in the GnomAD database, including 169 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 0.028 (169 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0795 is higher than 0.05.

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: 0.0280 AC: 4227 AN: 150942 Hom.: 170 Cov.: 32

Gnomad AFR AF: 0.0818

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0275

Gnomad ASJ AF: 0.0101

Gnomad EAS AF: 0.000773

Gnomad SAS AF: 0.00104

Gnomad FIN AF: 0.000195

Gnomad MID AF: 0.0226

Gnomad NFE AF: 0.00505

Gnomad OTH AF: 0.0354

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

GnomAD4 genome AF: 0.0280 AC: 4234 AN: 150990 Hom.: 169 Cov.: 32 AF XY: 0.0270 AC XY: 1990 AN XY: 73632

African (AFR) AF: 0.0818 AC: 3350 AN: 40964

American (AMR) AF: 0.0274 AC: 416 AN: 15166

Ashkenazi Jewish (ASJ) AF: 0.0101 AC: 35 AN: 3462

East Asian (EAS) AF: 0.000775 AC: 4 AN: 5162

South Asian (SAS) AF: 0.00105 AC: 5 AN: 4782

European-Finnish (FIN) AF: 0.000195 AC: 2 AN: 10258

Middle Eastern (MID) AF: 0.0245 AC: 7 AN: 286

European-Non Finnish (NFE) AF: 0.00504 AC: 342 AN: 67920

Other (OTH) AF: 0.0351 AC: 73 AN: 2078

Alfa AF: 0.0191 Hom.: 12

Bravo AF: 0.0343

Asia WGS AF: 0.00808 AC: 28 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.4
DANN	Benign	0.35
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs9658056; hg19: chr6-35309560;