4-122588266-G-T

Variant names:

• chr4-122588266-G-T
• rs6822844

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 0.101 in 152,242 control chromosomes in the GnomAD database, including 1,031 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 0.10 (1031 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730
• Publications: 165 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 (NFE) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15395 AN: 152124 Hom.: 1031 Cov.: 32

Gnomad AFR AF: 0.0286

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.0753

Gnomad ASJ AF: 0.0893

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.0786

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.0887

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

GnomAD4 genome AF: 0.101 AC: 15399 AN: 152242 Hom.: 1031 Cov.: 32 AF XY: 0.0973 AC XY: 7243 AN XY: 74446

African (AFR) AF: 0.0285 AC: 1185 AN: 41562

American (AMR) AF: 0.0752 AC: 1151 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0893 AC: 310 AN: 3472

East Asian (EAS) AF: 0.000964 AC: 5 AN: 5186

South Asian (SAS) AF: 0.0790 AC: 381 AN: 4820

European-Finnish (FIN) AF: 0.106 AC: 1124 AN: 10602

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10878 AN: 67990

Other (OTH) AF: 0.0873 AC: 184 AN: 2108

Alfa AF: 0.137 Hom.: 5972

Bravo AF: 0.0940

Asia WGS AF: 0.0360 AC: 127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.8
DANN	Benign	0.74
PhyloP100		0.073

Splicing

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

Other links and lift over

dbSNP: rs6822844; hg19: chr4-123509421;