6-32224554-A-G

Variant names:

• chr6-32224554-A-G
• rs3096702

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 0.716 in 152,104 control chromosomes in the GnomAD database, including 40,000 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 0.72 (40000 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.131
• Publications: 79 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.845 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.716 AC: 108822 AN: 151986 Hom.: 39951 Cov.: 32

Gnomad AFR AF: 0.852

Gnomad AMI AF: 0.740

Gnomad AMR AF: 0.692

Gnomad ASJ AF: 0.898

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.760

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

GnomAD4 genome AF: 0.716 AC: 108933 AN: 152104 Hom.: 40000 Cov.: 32 AF XY: 0.716 AC XY: 53248 AN XY: 74356

African (AFR) AF: 0.853 AC: 35392 AN: 41514

American (AMR) AF: 0.692 AC: 10567 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.898 AC: 3114 AN: 3468

East Asian (EAS) AF: 0.827 AC: 4259 AN: 5152

South Asian (SAS) AF: 0.803 AC: 3879 AN: 4828

European-Finnish (FIN) AF: 0.585 AC: 6191 AN: 10574

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.633 AC: 43002 AN: 67974

Other (OTH) AF: 0.760 AC: 1604 AN: 2110

Alfa AF: 0.665 Hom.: 109660

Bravo AF: 0.729

Asia WGS AF: 0.809 AC: 2811 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	7.8
DANN	Benign	0.55
PhyloP100		-0.13
PromoterAI		-0.014	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3096702; hg19: chr6-32192331;