rs9658056

chr6-35341783-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;