rs2066854

chr4-154614029-T-Achr4-154614029-T-G

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 0.256 in 151,992 control chromosomes in the GnomAD database, including 5,254 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 0.26 (5254 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.421

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.435 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: 0.256 AC: 38936 AN: 151874 Hom.: 5246 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.256 AC: 38974 AN: 151992 Hom.: 5254 Cov.: 32 AF XY: 0.259 AC XY: 19266 AN XY: 74290

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.217

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.306

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.220

Alfa AF: 0.243 Hom.: 639

Bravo AF: 0.252

Asia WGS AF: 0.319 AC: 1107 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	1.9
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2066854; hg19: chr4-155535181;