rs6469232

Variant names:

• chr8-109076012-G-A
• rs6469232

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.195 AC: 8069 AN: 41448

American (AMR) AF: 0.115 AC: 1759 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 498 AN: 3470

East Asian (EAS) AF: 0.0676 AC: 350 AN: 5178

South Asian (SAS) AF: 0.117 AC: 566 AN: 4820

European-Finnish (FIN) AF: 0.0838 AC: 882 AN: 10528

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.109 AC: 7440 AN: 68014

Other (OTH) AF: 0.146 AC: 309 AN: 2116

Alfa AF: 0.120 Hom.: 3820

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
PhyloP100		-0.039

Splicing

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

Other links and lift over

dbSNP: rs6469232; hg19: chr8-110088241;