4-27549447-G-T

Variant names:

• chr4-27549447-G-T
• rs4692241

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 0.209 in 152,010 control chromosomes in the GnomAD database, including 4,050 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 0.21 (4050 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.567 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: 0.209 AC: 31673 AN: 151892 Hom.: 4044 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.209 AC: 31719 AN: 152010 Hom.: 4050 Cov.: 32 AF XY: 0.212 AC XY: 15762 AN XY: 74308

African (AFR) AF: 0.271 AC: 11246 AN: 41440

American (AMR) AF: 0.274 AC: 4176 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 652 AN: 3472

East Asian (EAS) AF: 0.584 AC: 3017 AN: 5162

South Asian (SAS) AF: 0.104 AC: 502 AN: 4814

European-Finnish (FIN) AF: 0.187 AC: 1982 AN: 10578

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9366 AN: 67956

Other (OTH) AF: 0.231 AC: 489 AN: 2116

Alfa AF: 0.168 Hom.: 818

Bravo AF: 0.227

Asia WGS AF: 0.319 AC: 1108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.19
DANN	Benign	0.57
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4692241; hg19: chr4-27551069;