2-67997613-G-A

Variant names:

• chr2-67997613-G-A
• rs2221338

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 0.122 in 152,102 control chromosomes in the GnomAD database, including 2,073 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 0.12 (2073 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0910
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18487 AN: 151984 Hom.: 2071 Cov.: 32

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0862

Gnomad ASJ AF: 0.0971

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.0819

Gnomad FIN AF: 0.0147

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0435

Gnomad OTH AF: 0.0947

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

GnomAD4 genome AF: 0.122 AC: 18521 AN: 152102 Hom.: 2073 Cov.: 32 AF XY: 0.120 AC XY: 8941 AN XY: 74368

African (AFR) AF: 0.280 AC: 11587 AN: 41444

American (AMR) AF: 0.0861 AC: 1315 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0971 AC: 337 AN: 3470

East Asian (EAS) AF: 0.296 AC: 1526 AN: 5156

South Asian (SAS) AF: 0.0811 AC: 391 AN: 4820

European-Finnish (FIN) AF: 0.0147 AC: 156 AN: 10608

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0435 AC: 2961 AN: 68010

Other (OTH) AF: 0.0942 AC: 199 AN: 2112

Alfa AF: 0.0849 Hom.: 1409

Bravo AF: 0.137

Asia WGS AF: 0.157 AC: 545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.2
DANN	Benign	0.50
PhyloP100		-0.091

Splicing

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

Other links and lift over

dbSNP: rs2221338; hg19: chr2-68224745;