chr2-221192656-G-A

Position:

• chr2-221192656-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 0.892 in 152,238 control chromosomes in the GnomAD database, including 61,036 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 (61036 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.854

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.94 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: 0.892 AC: 135708 AN: 152122 Hom.: 61002 Cov.: 32

Gnomad AFR AF: 0.768

Gnomad AMI AF: 0.948

Gnomad AMR AF: 0.936

Gnomad ASJ AF: 0.970

Gnomad EAS AF: 0.929

Gnomad SAS AF: 0.963

Gnomad FIN AF: 0.970

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.933

Gnomad OTH AF: 0.901

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

GnomAD4 genome AF: 0.892 AC: 135791 AN: 152238 Hom.: 61036 Cov.: 32 AF XY: 0.895 AC XY: 66673 AN XY: 74456

Gnomad4 AFR AF: 0.768

Gnomad4 AMR AF: 0.936

Gnomad4 ASJ AF: 0.970

Gnomad4 EAS AF: 0.929

Gnomad4 SAS AF: 0.963

Gnomad4 FIN AF: 0.970

Gnomad4 NFE AF: 0.933

Gnomad4 OTH AF: 0.901

Alfa AF: 0.913 Hom.: 9569

Bravo AF: 0.883

Asia WGS AF: 0.938 AC: 3263 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	0.73
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1347038; hg19: chr2-222057376;