rs9494193

chr6-135262485-A-Cchr6-135262485-A-G

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 0.463 in 152,076 control chromosomes in the GnomAD database, including 18,947 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 0.46 (18947 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.746 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: 0.462 AC: 70248 AN: 151956 Hom.: 18911 Cov.: 32

Gnomad AFR AF: 0.752

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.463 AC: 70348 AN: 152076 Hom.: 18947 Cov.: 32 AF XY: 0.459 AC XY: 34153 AN XY: 74330

Gnomad4 AFR AF: 0.753

Gnomad4 AMR AF: 0.331

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.341

Gnomad4 SAS AF: 0.415

Gnomad4 FIN AF: 0.337

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.423

Alfa AF: 0.322 Hom.: 1804

Bravo AF: 0.470

Asia WGS AF: 0.412 AC: 1431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.041
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9494193; hg19: chr6-135583623;