rs9658056

Variant names:

• chr6-35341783-C-T
• rs9658056

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 0.028 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0280 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

Gnomad4 AFR AF: 0.0818

Gnomad4 AMR AF: 0.0274

Gnomad4 ASJ AF: 0.0101

Gnomad4 EAS AF: 0.000775

Gnomad4 SAS AF: 0.00105

Gnomad4 FIN AF: 0.000195

Gnomad4 NFE AF: 0.00504

Gnomad4 OTH AF: 0.0351

Alfa AF: 0.0166 Hom.: 10

Bravo AF: 0.0343

Asia WGS AF: 0.00808 AC: 28 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9658056; hg19: chr6-35309560;