rs3129868

Positions:

• chr6-32436600-A-C

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 152,122 control chromosomes in the GnomAD database, including 60,917 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 (60917 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93

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 (AFR) allele frequency at 95% confidence interval = 0.943 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.894 AC: 135865 AN: 152004 Hom.: 60863 Cov.: 31

Gnomad AFR AF: 0.951

Gnomad AMI AF: 0.913

Gnomad AMR AF: 0.919

Gnomad ASJ AF: 0.933

Gnomad EAS AF: 0.885

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: 135978 AN: 152122 Hom.: 60917 Cov.: 31 AF XY: 0.893 AC XY: 66433 AN XY: 74364

Gnomad4 AFR AF: 0.951

Gnomad4 AMR AF: 0.919

Gnomad4 ASJ AF: 0.933

Gnomad4 EAS AF: 0.885

Gnomad4 SAS AF: 0.883

Gnomad4 FIN AF: 0.871

Gnomad4 NFE AF: 0.855

Gnomad4 OTH AF: 0.918

Alfa AF: 0.877 Hom.: 35082

Bravo AF: 0.903

Asia WGS AF: 0.901 AC: 3134 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	0.040
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3129868; hg19: chr6-32404377;