chr2-119152738-C-T

Variant names:

• chr2-119152738-C-T
• rs745888

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 0.241 in 152,144 control chromosomes in the GnomAD database, including 5,471 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 0.24 (5471 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36612 AN: 152026 Hom.: 5470 Cov.: 33

Gnomad AFR AF: 0.0885

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.241 AC: 36623 AN: 152144 Hom.: 5471 Cov.: 33 AF XY: 0.248 AC XY: 18421 AN XY: 74380

African (AFR) AF: 0.0884 AC: 3670 AN: 41530

American (AMR) AF: 0.237 AC: 3617 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.307 AC: 1064 AN: 3468

East Asian (EAS) AF: 0.590 AC: 3051 AN: 5172

South Asian (SAS) AF: 0.298 AC: 1434 AN: 4818

European-Finnish (FIN) AF: 0.368 AC: 3891 AN: 10562

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.277 AC: 18825 AN: 67990

Other (OTH) AF: 0.276 AC: 583 AN: 2112

Alfa AF: 0.266 Hom.: 9395

Bravo AF: 0.228

Asia WGS AF: 0.410 AC: 1427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.0
DANN	Benign	0.80
PhyloP100		0.064

Splicing

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

Other links and lift over

dbSNP: rs745888; hg19: chr2-119910314;