4-55125972-C-T

Variant names:

• chr4-55125972-C-T
• rs2239702

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 0.236 in 152,086 control chromosomes in the GnomAD database, including 4,313 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 0.24 (4313 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.984
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.247 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: 0.236 AC: 35878 AN: 151968 Hom.: 4312 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.236 AC: 35881 AN: 152086 Hom.: 4313 Cov.: 32 AF XY: 0.234 AC XY: 17368 AN XY: 74358

African (AFR) AF: 0.231 AC: 9606 AN: 41512

American (AMR) AF: 0.197 AC: 3008 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1046 AN: 3470

East Asian (EAS) AF: 0.179 AC: 921 AN: 5134

South Asian (SAS) AF: 0.244 AC: 1176 AN: 4822

European-Finnish (FIN) AF: 0.222 AC: 2351 AN: 10572

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 16996 AN: 67972

Other (OTH) AF: 0.221 AC: 467 AN: 2114

Alfa AF: 0.242 Hom.: 2435

Bravo AF: 0.232

Asia WGS AF: 0.193 AC: 669 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.3
DANN	Benign	0.93
PhyloP100		-0.98
PromoterAI		0.00020	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2239702; hg19: chr4-55992139;