rs2857154

Positions:

• chr6-32794839-A-G

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 0.673 in 152,090 control chromosomes in the GnomAD database, including 34,646 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 (34646 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.801

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.32794839A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.673 AC: 102260 AN: 151972 Hom.: 34637 Cov.: 31

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.822

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.719

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.768

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.673 AC: 102306 AN: 152090 Hom.: 34646 Cov.: 31 AF XY: 0.680 AC XY: 50509 AN XY: 74326

Gnomad4 AFR AF: 0.651

Gnomad4 AMR AF: 0.656

Gnomad4 ASJ AF: 0.708

Gnomad4 EAS AF: 0.719

Gnomad4 SAS AF: 0.808

Gnomad4 FIN AF: 0.768

Gnomad4 NFE AF: 0.657

Gnomad4 OTH AF: 0.683

Alfa AF: 0.656 Hom.: 9504

Bravo AF: 0.659

Asia WGS AF: 0.749 AC: 2607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.7
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2857154; hg19: chr6-32762616;