chr4-18918541-C-T

Position:

• chr4-18918541-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 0.409 in 151,794 control chromosomes in the GnomAD database, including 12,873 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 0.41 (12873 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.741

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.609 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: 0.409 AC: 62059 AN: 151676 Hom.: 12848 Cov.: 31

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.409 AC: 62122 AN: 151794 Hom.: 12873 Cov.: 31 AF XY: 0.415 AC XY: 30745 AN XY: 74142

Gnomad4 AFR AF: 0.385

Gnomad4 AMR AF: 0.446

Gnomad4 ASJ AF: 0.505

Gnomad4 EAS AF: 0.627

Gnomad4 SAS AF: 0.489

Gnomad4 FIN AF: 0.379

Gnomad4 NFE AF: 0.394

Gnomad4 OTH AF: 0.447

Alfa AF: 0.399 Hom.: 6253

Bravo AF: 0.413

Asia WGS AF: 0.540 AC: 1877 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.78
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1452554; hg19: chr4-18920164;