rs9492645

chr6-130565292-G-Achr6-130565292-G-Cchr6-130565292-G-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 0.0673 in 152,070 control chromosomes in the GnomAD database, including 488 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 0.067 (488 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.132

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.126 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: 0.0672 AC: 10213 AN: 151952 Hom.: 483 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0448

Gnomad ASJ AF: 0.0968

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0495

Gnomad FIN AF: 0.0379

Gnomad MID AF: 0.0897

Gnomad NFE AF: 0.0449

Gnomad OTH AF: 0.0612

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

GnomAD4 genome AF: 0.0673 AC: 10238 AN: 152070 Hom.: 488 Cov.: 32 AF XY: 0.0660 AC XY: 4903 AN XY: 74338

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.0448

Gnomad4 ASJ AF: 0.0968

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.0500

Gnomad4 FIN AF: 0.0379

Gnomad4 NFE AF: 0.0450

Gnomad4 OTH AF: 0.0605

Alfa AF: 0.0173 Hom.: 8

Bravo AF: 0.0682

Asia WGS AF: 0.0270 AC: 94 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.74
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9492645; hg19: chr6-130886437;