4-154602694-A-T

Variant names:

• chr4-154602694-A-T
• rs1118823

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 0.601 in 151,988 control chromosomes in the GnomAD database, including 28,351 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 0.60 (28351 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.916
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.782 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: 0.601 AC: 91250 AN: 151868 Hom.: 28347 Cov.: 32

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.803

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.601 AC: 91283 AN: 151988 Hom.: 28351 Cov.: 32 AF XY: 0.597 AC XY: 44312 AN XY: 74276

African (AFR) AF: 0.446 AC: 18465 AN: 41438

American (AMR) AF: 0.531 AC: 8106 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.596 AC: 2068 AN: 3468

East Asian (EAS) AF: 0.802 AC: 4158 AN: 5182

South Asian (SAS) AF: 0.623 AC: 3001 AN: 4816

European-Finnish (FIN) AF: 0.612 AC: 6452 AN: 10550

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.691 AC: 46975 AN: 67954

Other (OTH) AF: 0.606 AC: 1278 AN: 2108

Alfa AF: 0.632 Hom.: 3655

Bravo AF: 0.592

Asia WGS AF: 0.654 AC: 2269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.27
DANN	Benign	0.48
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs1118823; hg19: chr4-155523846;