4-122448621-T-G

Variant names:

• chr4-122448621-T-G
• rs3136534

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 0.289 in 151,444 control chromosomes in the GnomAD database, including 7,470 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 0.29 (7470 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.46 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: 0.290 AC: 43813 AN: 151330 Hom.: 7469 Cov.: 27

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.289 AC: 43813 AN: 151444 Hom.: 7470 Cov.: 27 AF XY: 0.296 AC XY: 21913 AN XY: 73968

African (AFR) AF: 0.116 AC: 4784 AN: 41384

American (AMR) AF: 0.396 AC: 6024 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 735 AN: 3468

East Asian (EAS) AF: 0.475 AC: 2444 AN: 5140

South Asian (SAS) AF: 0.262 AC: 1253 AN: 4786

European-Finnish (FIN) AF: 0.468 AC: 4841 AN: 10334

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.338 AC: 22932 AN: 67810

Other (OTH) AF: 0.271 AC: 570 AN: 2104

Alfa AF: 0.283 Hom.: 1705

Bravo AF: 0.280

Asia WGS AF: 0.301 AC: 1045 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.2
DANN	Benign	0.65
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs3136534; hg19: chr4-123369776;