rs3096702

chr6-32224554-A-Gchr6-32224554-A-T

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 0.716 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.716 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

Gnomad4 AFR AF: 0.853

Gnomad4 AMR AF: 0.692

Gnomad4 ASJ AF: 0.898

Gnomad4 EAS AF: 0.827

Gnomad4 SAS AF: 0.803

Gnomad4 FIN AF: 0.585

Gnomad4 NFE AF: 0.633

Gnomad4 OTH AF: 0.760

Alfa AF: 0.665 Hom.: 40035

Bravo AF: 0.729

Asia WGS AF: 0.809 AC: 2811 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	7.8
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3096702; hg19: chr6-32192331;