2-227720182-T-G

Variant names:

• chr2-227720182-T-G
• rs11691652

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 0.28 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
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.250 AC: 10376 AN: 41504

American (AMR) AF: 0.234 AC: 3584 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 727 AN: 3470

East Asian (EAS) AF: 0.218 AC: 1132 AN: 5184

South Asian (SAS) AF: 0.240 AC: 1156 AN: 4824

European-Finnish (FIN) AF: 0.266 AC: 2813 AN: 10576

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.319 AC: 21692 AN: 67996

Other (OTH) AF: 0.290 AC: 613 AN: 2112

Alfa AF: 0.301 Hom.: 15019

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
PhyloP100		-0.0070

Splicing

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

Other links and lift over

dbSNP: rs11691652; hg19: chr2-228584898;