rs6477233

Variant names:

• chr9-7774774-T-A
• rs6477233

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 0.429 in 151,798 control chromosomes in the GnomAD database, including 15,599 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 0.43 (15599 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.360

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.655 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: 0.429 AC: 65043 AN: 151680 Hom.: 15568 Cov.: 32

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.429 AC: 65129 AN: 151798 Hom.: 15599 Cov.: 32 AF XY: 0.424 AC XY: 31430 AN XY: 74160

Gnomad4 AFR AF: 0.662

Gnomad4 AMR AF: 0.363

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.311

Gnomad4 FIN AF: 0.357

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.397

Alfa AF: 0.405 Hom.: 1694

Bravo AF: 0.437

Asia WGS AF: 0.294 AC: 1020 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.0
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6477233; hg19: chr9-7774774; COSMIC: COSV69445548;