rs2070897

chr4-99322153-G-A

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 0.569 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.569 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

Gnomad4 AFR AF: 0.418

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.693

Gnomad4 EAS AF: 0.825

Gnomad4 SAS AF: 0.633

Gnomad4 FIN AF: 0.553

Gnomad4 NFE AF: 0.649

Gnomad4 OTH AF: 0.597

Alfa AF: 0.588 Hom.: 3845

Bravo AF: 0.553

Asia WGS AF: 0.589 AC: 2049 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.37
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2070897; hg19: chr4-100243310;