chr2-233774704-A-G

Position:

• chr2-233774704-A-G

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 0.115 in 152,130 control chromosomes in the GnomAD database, including 1,313 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 (1313 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.241

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17555 AN: 152012 Hom.: 1308 Cov.: 31

Gnomad AFR AF: 0.0326

Gnomad AMI AF: 0.0791

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.115 AC: 17565 AN: 152130 Hom.: 1313 Cov.: 31 AF XY: 0.117 AC XY: 8718 AN XY: 74360

Gnomad4 AFR AF: 0.0326

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.198

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.132

Alfa AF: 0.133 Hom.: 1396

Bravo AF: 0.111

Asia WGS AF: 0.198 AC: 687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11563250; hg19: chr2-234683350;