4-154528477-C-T

Variant names:

• chr4-154528477-C-T
• rs7689945

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 0.524 in 151,944 control chromosomes in the GnomAD database, including 21,159 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 0.52 (21159 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.252
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.672 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: 0.524 AC: 79597 AN: 151826 Hom.: 21147 Cov.: 32

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.691

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.524 AC: 79642 AN: 151944 Hom.: 21159 Cov.: 32 AF XY: 0.525 AC XY: 38973 AN XY: 74262

African (AFR) AF: 0.506 AC: 20947 AN: 41422

American (AMR) AF: 0.457 AC: 6986 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1767 AN: 3468

East Asian (EAS) AF: 0.691 AC: 3583 AN: 5186

South Asian (SAS) AF: 0.604 AC: 2910 AN: 4820

European-Finnish (FIN) AF: 0.516 AC: 5424 AN: 10518

Middle Eastern (MID) AF: 0.531 AC: 155 AN: 292

European-Non Finnish (NFE) AF: 0.534 AC: 36309 AN: 67934

Other (OTH) AF: 0.530 AC: 1119 AN: 2112

Alfa AF: 0.533 Hom.: 88589

Bravo AF: 0.518

Asia WGS AF: 0.632 AC: 2189 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.22
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs7689945; hg19: chr4-155449629;