chr2-221192656-G-A

Variant names:

• chr2-221192656-G-A
• rs1347038

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 0.892 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.768 AC: 31888 AN: 41514

American (AMR) AF: 0.936 AC: 14310 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.970 AC: 3367 AN: 3472

East Asian (EAS) AF: 0.929 AC: 4807 AN: 5176

South Asian (SAS) AF: 0.963 AC: 4650 AN: 4828

European-Finnish (FIN) AF: 0.970 AC: 10293 AN: 10612

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.933 AC: 63449 AN: 68024

Other (OTH) AF: 0.901 AC: 1905 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.73
DANN	Benign	0.17
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs1347038; hg19: chr2-222057376;