rs2070897

Variant names:

• chr4-99322153-G-A
• rs2070897

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 0.569 in 152,012 control chromosomes in the GnomAD database, including 25,668 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 0.57 (25668 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.722
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86405 AN: 151894 Hom.: 25669 Cov.: 33

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.569 AC: 86421 AN: 152012 Hom.: 25668 Cov.: 33 AF XY: 0.564 AC XY: 41887 AN XY: 74312

African (AFR) AF: 0.418 AC: 17317 AN: 41424

American (AMR) AF: 0.472 AC: 7196 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.693 AC: 2403 AN: 3468

East Asian (EAS) AF: 0.825 AC: 4264 AN: 5168

South Asian (SAS) AF: 0.633 AC: 3051 AN: 4820

European-Finnish (FIN) AF: 0.553 AC: 5843 AN: 10564

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.649 AC: 44157 AN: 67988

Other (OTH) AF: 0.597 AC: 1261 AN: 2114

Alfa AF: 0.582 Hom.: 3916

Bravo AF: 0.553

Asia WGS AF: 0.589 AC: 2049 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.37
DANN	Benign	0.31
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs2070897; hg19: chr4-100243310;