rs9498069

chr6-148614507-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 0.0573 in 152,220 control chromosomes in the GnomAD database, including 307 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 0.057 (307 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.142 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: 0.0573 AC: 8715 AN: 152104 Hom.: 306 Cov.: 32

Gnomad AFR AF: 0.0796

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.0312

Gnomad ASJ AF: 0.0412

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.0788

Gnomad FIN AF: 0.0853

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0373

Gnomad OTH AF: 0.0455

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

GnomAD4 genome AF: 0.0573 AC: 8728 AN: 152220 Hom.: 307 Cov.: 32 AF XY: 0.0603 AC XY: 4485 AN XY: 74424

Gnomad4 AFR AF: 0.0797

Gnomad4 AMR AF: 0.0311

Gnomad4 ASJ AF: 0.0412

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.0787

Gnomad4 FIN AF: 0.0853

Gnomad4 NFE AF: 0.0373

Gnomad4 OTH AF: 0.0445

Alfa AF: 0.0451 Hom.: 16

Bravo AF: 0.0535

Asia WGS AF: 0.106 AC: 369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	1.3
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9498069; hg19: chr6-148935643;