4-154503079-T-C

Variant names:

• chr4-154503079-T-C
• rs4323084

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 0.757 in 151,926 control chromosomes in the GnomAD database, including 44,403 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 0.76 (44403 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.349
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.83 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: 0.757 AC: 114860 AN: 151808 Hom.: 44364 Cov.: 31

Gnomad AFR AF: 0.838

Gnomad AMI AF: 0.687

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.738

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.758

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.827

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.774

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

GnomAD4 genome AF: 0.757 AC: 114956 AN: 151926 Hom.: 44403 Cov.: 31 AF XY: 0.750 AC XY: 55663 AN XY: 74234

African (AFR) AF: 0.838 AC: 34701 AN: 41422

American (AMR) AF: 0.729 AC: 11134 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.738 AC: 2560 AN: 3470

East Asian (EAS) AF: 0.264 AC: 1358 AN: 5144

South Asian (SAS) AF: 0.756 AC: 3642 AN: 4816

European-Finnish (FIN) AF: 0.672 AC: 7083 AN: 10544

Middle Eastern (MID) AF: 0.824 AC: 239 AN: 290

European-Non Finnish (NFE) AF: 0.765 AC: 51972 AN: 67946

Other (OTH) AF: 0.777 AC: 1642 AN: 2114

Alfa AF: 0.759 Hom.: 184769

Bravo AF: 0.758

Asia WGS AF: 0.580 AC: 2015 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.36
DANN	Benign	0.63
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs4323084; hg19: chr4-155424231;