chr2-85536883-C-T

Variant names:

• chr2-85536883-C-T
• rs3755014

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 0.531 in 152,042 control chromosomes in the GnomAD database, including 22,835 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 0.53 (22835 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.17

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.73 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: 0.531 AC: 80618 AN: 151924 Hom.: 22800 Cov.: 32

Gnomad AFR AF: 0.737

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.531 AC: 80708 AN: 152042 Hom.: 22835 Cov.: 32 AF XY: 0.527 AC XY: 39140 AN XY: 74308

Gnomad4 AFR AF: 0.737

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.392

Gnomad4 SAS AF: 0.396

Gnomad4 FIN AF: 0.458

Gnomad4 NFE AF: 0.467

Gnomad4 OTH AF: 0.521

Alfa AF: 0.486 Hom.: 4282

Bravo AF: 0.536

Asia WGS AF: 0.441 AC: 1536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.33
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3755014; hg19: chr2-85764006;