rs896010

Positions:

• chr8-83072575-A-G
• chr8-83072575-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 0.865 in 152,182 control chromosomes in the GnomAD database, including 57,046 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 0.86 (57046 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.88 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: 0.865 AC: 131497 AN: 152064 Hom.: 57004 Cov.: 32

Gnomad AFR AF: 0.827

Gnomad AMI AF: 0.833

Gnomad AMR AF: 0.858

Gnomad ASJ AF: 0.785

Gnomad EAS AF: 0.844

Gnomad SAS AF: 0.854

Gnomad FIN AF: 0.933

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.885

Gnomad OTH AF: 0.863

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

GnomAD4 genome AF: 0.865 AC: 131594 AN: 152182 Hom.: 57046 Cov.: 32 AF XY: 0.866 AC XY: 64428 AN XY: 74402

Gnomad4 AFR AF: 0.827

Gnomad4 AMR AF: 0.858

Gnomad4 ASJ AF: 0.785

Gnomad4 EAS AF: 0.843

Gnomad4 SAS AF: 0.855

Gnomad4 FIN AF: 0.933

Gnomad4 NFE AF: 0.885

Gnomad4 OTH AF: 0.863

Alfa AF: 0.877 Hom.: 116857

Bravo AF: 0.857

Asia WGS AF: 0.864 AC: 3006 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.4
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs896010; hg19: chr8-83984810;