4-154552018-C-T

Variant names:

• chr4-154552018-C-T
• rs9997519

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 0.16 in 152,056 control chromosomes in the GnomAD database, including 2,242 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 0.16 (2242 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.265 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: 0.160 AC: 24305 AN: 151938 Hom.: 2232 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.0545

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.160 AC: 24320 AN: 152056 Hom.: 2242 Cov.: 32 AF XY: 0.162 AC XY: 12076 AN XY: 74318

African (AFR) AF: 0.125 AC: 5188 AN: 41488

American (AMR) AF: 0.272 AC: 4154 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 438 AN: 3470

East Asian (EAS) AF: 0.0542 AC: 281 AN: 5180

South Asian (SAS) AF: 0.145 AC: 696 AN: 4814

European-Finnish (FIN) AF: 0.186 AC: 1965 AN: 10548

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 11000 AN: 67966

Other (OTH) AF: 0.173 AC: 366 AN: 2112

Alfa AF: 0.157 Hom.: 3510

Bravo AF: 0.162

Asia WGS AF: 0.127 AC: 441 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.6
DANN	Benign	0.68
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs9997519; hg19: chr4-155473170;