rs2010016

Variant names:

• chr8-98056026-A-C
• rs2010016

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0919 in 152,266 control chromosomes in the GnomAD database, including 789 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 0.092 (789 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.51
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.182 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: 0.0919 AC: 13990 AN: 152148 Hom.: 784 Cov.: 33

Gnomad AFR AF: 0.0317

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.0893

Gnomad FIN AF: 0.0815

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.0919 AC: 13999 AN: 152266 Hom.: 789 Cov.: 33 AF XY: 0.0932 AC XY: 6938 AN XY: 74444

African (AFR) AF: 0.0320 AC: 1328 AN: 41544

American (AMR) AF: 0.130 AC: 1981 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 611 AN: 3470

East Asian (EAS) AF: 0.192 AC: 994 AN: 5180

South Asian (SAS) AF: 0.0900 AC: 435 AN: 4832

European-Finnish (FIN) AF: 0.0815 AC: 865 AN: 10610

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7450 AN: 68020

Other (OTH) AF: 0.108 AC: 228 AN: 2112

Alfa AF: 0.0976 Hom.: 132

Bravo AF: 0.0958

Asia WGS AF: 0.131 AC: 460 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	8.2
DANN	Benign	0.53
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs2010016; hg19: chr8-99068254;