4-26480399-C-T

Variant names:

• chr4-26480399-C-T
• rs2854030

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 0.327 in 151,850 control chromosomes in the GnomAD database, including 8,394 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 0.33 (8394 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.370

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.398 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: 0.327 AC: 49555 AN: 151732 Hom.: 8373 Cov.: 31

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.327 AC: 49633 AN: 151850 Hom.: 8394 Cov.: 31 AF XY: 0.329 AC XY: 24445 AN XY: 74224

Gnomad4 AFR AF: 0.395

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.356

Gnomad4 SAS AF: 0.414

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.290

Gnomad4 OTH AF: 0.356

Alfa AF: 0.302 Hom.: 14600

Bravo AF: 0.322

Asia WGS AF: 0.397 AC: 1379 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.3
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2854030; hg19: chr4-26482021;