rs2055451

Positions:

• chr3-79792979-G-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 0.299 in 151,844 control chromosomes in the GnomAD database, including 6,882 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 0.30 (6882 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45371 AN: 151724 Hom.: 6876 Cov.: 32

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.299 AC: 45411 AN: 151844 Hom.: 6882 Cov.: 32 AF XY: 0.298 AC XY: 22126 AN XY: 74214

Gnomad4 AFR AF: 0.340

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.287

Gnomad4 OTH AF: 0.276

Alfa AF: 0.293 Hom.: 2868

Bravo AF: 0.304

Asia WGS AF: 0.316 AC: 1097 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	15
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2055451; hg19: chr3-79842129;