rs2572886

Variant names:

• chr8-142821739-A-G
• rs2572886

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 0.886 in 152,184 control chromosomes in the GnomAD database, including 60,328 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 0.89 (60328 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.945 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: 0.886 AC: 134746 AN: 152066 Hom.: 60302 Cov.: 32

Gnomad AFR AF: 0.756

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.903

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.767

Gnomad SAS AF: 0.929

Gnomad FIN AF: 0.980

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.951

Gnomad OTH AF: 0.895

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

GnomAD4 genome AF: 0.886 AC: 134826 AN: 152184 Hom.: 60328 Cov.: 32 AF XY: 0.889 AC XY: 66107 AN XY: 74400

African (AFR) AF: 0.756 AC: 31366 AN: 41488

American (AMR) AF: 0.903 AC: 13811 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.875 AC: 3037 AN: 3470

East Asian (EAS) AF: 0.767 AC: 3960 AN: 5160

South Asian (SAS) AF: 0.930 AC: 4478 AN: 4816

European-Finnish (FIN) AF: 0.980 AC: 10413 AN: 10628

Middle Eastern (MID) AF: 0.939 AC: 276 AN: 294

European-Non Finnish (NFE) AF: 0.951 AC: 64689 AN: 68008

Other (OTH) AF: 0.894 AC: 1887 AN: 2110

Alfa AF: 0.930 Hom.: 211777

Bravo AF: 0.873

Asia WGS AF: 0.825 AC: 2871 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	0.81
DANN	Benign	0.35
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs2572886; hg19: chr8-143903155;