rs3129889

chr6-32445768-G-Achr6-32445768-G-Cchr6-32445768-G-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 0.906 in 152,218 control chromosomes in the GnomAD database, including 62,668 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 0.91 (62668 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 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: 0.906 AC: 137815 AN: 152100 Hom.: 62615 Cov.: 31

Gnomad AFR AF: 0.953

Gnomad AMI AF: 0.913

Gnomad AMR AF: 0.928

Gnomad ASJ AF: 0.978

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.980

Gnomad FIN AF: 0.871

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.861

Gnomad OTH AF: 0.932

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

GnomAD4 genome AF: 0.906 AC: 137926 AN: 152218 Hom.: 62668 Cov.: 31 AF XY: 0.908 AC XY: 67543 AN XY: 74416

Gnomad4 AFR AF: 0.953

Gnomad4 AMR AF: 0.928

Gnomad4 ASJ AF: 0.978

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.981

Gnomad4 FIN AF: 0.871

Gnomad4 NFE AF: 0.861

Gnomad4 OTH AF: 0.933

Alfa AF: 0.881 Hom.: 85322

Bravo AF: 0.913

Asia WGS AF: 0.982 AC: 3414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.24
Dann	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3129889; hg19: chr6-32413545;