rs3129860

Variant names:

• chr6-32433302-A-G
• rs3129860

Your query was ambiguous. Multiple possible variants found:

• chr6-32433302-A-G
• chr6-32433302-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 0.894 in 152,230 control chromosomes in the GnomAD database, including 60,951 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 0.89 (60951 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.944 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: 0.894 AC: 135949 AN: 152112 Hom.: 60897 Cov.: 32

Gnomad AFR AF: 0.952

Gnomad AMI AF: 0.913

Gnomad AMR AF: 0.918

Gnomad ASJ AF: 0.933

Gnomad EAS AF: 0.884

Gnomad SAS AF: 0.883

Gnomad FIN AF: 0.871

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.855

Gnomad OTH AF: 0.916

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

GnomAD4 genome AF: 0.894 AC: 136062 AN: 152230 Hom.: 60951 Cov.: 32 AF XY: 0.893 AC XY: 66471 AN XY: 74416

Gnomad4 AFR AF: 0.951

Gnomad4 AMR AF: 0.919

Gnomad4 ASJ AF: 0.933

Gnomad4 EAS AF: 0.884

Gnomad4 SAS AF: 0.883

Gnomad4 FIN AF: 0.871

Gnomad4 NFE AF: 0.855

Gnomad4 OTH AF: 0.918

Alfa AF: 0.866 Hom.: 34839

Bravo AF: 0.903

Asia WGS AF: 0.904 AC: 3145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.13
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3129860; hg19: chr6-32401079;