rs2857129

Variant names:

• chr6-32808846-A-T
• rs2857129

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 0.671 in 152,046 control chromosomes in the GnomAD database, including 34,487 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 0.67 (34487 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.782 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: 0.671 AC: 102015 AN: 151928 Hom.: 34480 Cov.: 32

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.719

Gnomad SAS AF: 0.804

Gnomad FIN AF: 0.768

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.681

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

GnomAD4 genome AF: 0.671 AC: 102059 AN: 152046 Hom.: 34487 Cov.: 32 AF XY: 0.678 AC XY: 50403 AN XY: 74334

Gnomad4 AFR AF: 0.647

Gnomad4 AMR AF: 0.653

Gnomad4 ASJ AF: 0.709

Gnomad4 EAS AF: 0.719

Gnomad4 SAS AF: 0.804

Gnomad4 FIN AF: 0.768

Gnomad4 NFE AF: 0.657

Gnomad4 OTH AF: 0.683

Alfa AF: 0.665 Hom.: 4187

Bravo AF: 0.657

Asia WGS AF: 0.741 AC: 2580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2857129; hg19: chr6-32776623;