rs6477233

Positions:

• chr9-7774774-T-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;