rs6469232

chr8-109076012-G-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 0.131 in 152,060 control chromosomes in the GnomAD database, including 1,484 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 0.13 (1484 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.191 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: 0.131 AC: 19953 AN: 151946 Hom.: 1482 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.0747

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.0676

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.0838

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.131 AC: 19973 AN: 152060 Hom.: 1484 Cov.: 32 AF XY: 0.131 AC XY: 9707 AN XY: 74320

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.0676

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.0838

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.146

Alfa AF: 0.117 Hom.: 2291

Bravo AF: 0.136

Asia WGS AF: 0.113 AC: 394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.8
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: rs6469232; hg19: chr8-110088241;