rs4852655

Positions:

• chr2-82008520-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 0.401 in 152,042 control chromosomes in the GnomAD database, including 13,582 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 0.40 (13582 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.22

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.558 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: 0.401 AC: 60876 AN: 151924 Hom.: 13574 Cov.: 33

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.401 AC: 60900 AN: 152042 Hom.: 13582 Cov.: 33 AF XY: 0.403 AC XY: 29956 AN XY: 74296

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.513

Gnomad4 ASJ AF: 0.420

Gnomad4 EAS AF: 0.575

Gnomad4 SAS AF: 0.541

Gnomad4 FIN AF: 0.424

Gnomad4 NFE AF: 0.476

Gnomad4 OTH AF: 0.440

Alfa AF: 0.412 Hom.: 3098

Bravo AF: 0.397

Asia WGS AF: 0.553 AC: 1926 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.13
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4852655; hg19: chr2-82235644;