4-154969089-C-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 0.606 in 151,982 control chromosomes in the GnomAD database, including 28,285 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 0.61 (28285 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.148

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.605 AC: 91934 AN: 151864 Hom.: 28242 Cov.: 31

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.719

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.606 AC: 92026 AN: 151982 Hom.: 28285 Cov.: 31 AF XY: 0.608 AC XY: 45175 AN XY: 74288

Gnomad4 AFR AF: 0.697

Gnomad4 AMR AF: 0.572

Gnomad4 ASJ AF: 0.498

Gnomad4 EAS AF: 0.743

Gnomad4 SAS AF: 0.720

Gnomad4 FIN AF: 0.606

Gnomad4 NFE AF: 0.545

Gnomad4 OTH AF: 0.576

Alfa AF: 0.566 Hom.: 7927

Bravo AF: 0.603

Asia WGS AF: 0.690 AC: 2391 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.33
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6837016; hg19: chr4-155890241;