2-235220307-A-G

Variant names:

• chr2-235220307-A-G
• rs1991705

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 0.872 in 152,218 control chromosomes in the GnomAD database, including 58,409 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 0.87 (58409 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.58

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 = 0.976 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: 0.872 AC: 132636 AN: 152100 Hom.: 58363 Cov.: 33

Gnomad AFR AF: 0.759

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.831

Gnomad ASJ AF: 0.890

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.911

Gnomad FIN AF: 0.938

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.927

Gnomad OTH AF: 0.865

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

GnomAD4 genome AF: 0.872 AC: 132739 AN: 152218 Hom.: 58409 Cov.: 33 AF XY: 0.872 AC XY: 64901 AN XY: 74424

Gnomad4 AFR AF: 0.759

Gnomad4 AMR AF: 0.832

Gnomad4 ASJ AF: 0.890

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.912

Gnomad4 FIN AF: 0.938

Gnomad4 NFE AF: 0.927

Gnomad4 OTH AF: 0.867

Alfa AF: 0.909 Hom.: 61986

Bravo AF: 0.859

Asia WGS AF: 0.940 AC: 3265 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	0.015
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1991705; hg19: chr2-236128951;