rs2857129

chr6-32808846-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 0.671 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;