2-227720182-T-G

Variant names:

• chr2-227720182-T-G
• rs11691652

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 0.28 in 152,156 control chromosomes in the GnomAD database, including 6,113 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 0.28 (6113 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.315 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: 0.280 AC: 42556 AN: 152038 Hom.: 6112 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.280 AC: 42564 AN: 152156 Hom.: 6113 Cov.: 32 AF XY: 0.274 AC XY: 20360 AN XY: 74394

Gnomad4 AFR AF: 0.250

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.266

Gnomad4 NFE AF: 0.319

Gnomad4 OTH AF: 0.290

Alfa AF: 0.300 Hom.: 10102

Bravo AF: 0.277

Asia WGS AF: 0.230 AC: 799 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.1
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11691652; hg19: chr2-228584898;