chr4-154602694-A-T

Position:

• chr4-154602694-A-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.446

Gnomad4 AMR AF: 0.531

Gnomad4 ASJ AF: 0.596

Gnomad4 EAS AF: 0.802

Gnomad4 SAS AF: 0.623

Gnomad4 FIN AF: 0.612

Gnomad4 NFE AF: 0.691

Gnomad4 OTH AF: 0.606

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1118823; hg19: chr4-155523846;