2-152892854-C-T

Variant names:

• chr2-152892854-C-T
• rs78683678

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 0.0573 in 152,162 control chromosomes in the GnomAD database, including 344 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 0.057 (344 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.352
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0832 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0574 AC: 8727 AN: 152044 Hom.: 343 Cov.: 32

Gnomad AFR AF: 0.0150

Gnomad AMI AF: 0.0890

Gnomad AMR AF: 0.0411

Gnomad ASJ AF: 0.0611

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0481

Gnomad FIN AF: 0.0998

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0850

Gnomad OTH AF: 0.0532

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

GnomAD4 genome AF: 0.0573 AC: 8725 AN: 152162 Hom.: 344 Cov.: 32 AF XY: 0.0577 AC XY: 4293 AN XY: 74390

African (AFR) AF: 0.0149 AC: 620 AN: 41530

American (AMR) AF: 0.0411 AC: 628 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0611 AC: 212 AN: 3472

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5176

South Asian (SAS) AF: 0.0483 AC: 233 AN: 4822

European-Finnish (FIN) AF: 0.0998 AC: 1055 AN: 10566

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0850 AC: 5780 AN: 67996

Other (OTH) AF: 0.0517 AC: 109 AN: 2108

Alfa AF: 0.0436 Hom.: 38

Bravo AF: 0.0495

Asia WGS AF: 0.0230 AC: 80 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	8.3
DANN	Benign	0.77
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs78683678; hg19: chr2-153749368;