chr2-233855851-C-T

Position:

• chr2-233855851-C-T

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 0.718 in 151,962 control chromosomes in the GnomAD database, including 39,573 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 0.72 (39573 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.293

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.809 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.718 AC: 109033 AN: 151844 Hom.: 39521 Cov.: 30

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.718

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.718 AC: 109150 AN: 151962 Hom.: 39573 Cov.: 30 AF XY: 0.716 AC XY: 53168 AN XY: 74266

Gnomad4 AFR AF: 0.816

Gnomad4 AMR AF: 0.684

Gnomad4 ASJ AF: 0.702

Gnomad4 EAS AF: 0.727

Gnomad4 SAS AF: 0.544

Gnomad4 FIN AF: 0.720

Gnomad4 NFE AF: 0.678

Gnomad4 OTH AF: 0.728

Alfa AF: 0.707 Hom.: 6573

Bravo AF: 0.724

Asia WGS AF: 0.623 AC: 2170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.65
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs887062; hg19: chr2-234764497;