rs6469232

Variant names:

• chr8-109076012-G-A
• rs6469232

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;