2-85335049-C-T

Variant names:

• chr2-85335049-C-T
• rs3923229

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 0.811 in 152,178 control chromosomes in the GnomAD database, including 50,636 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 0.81 (50636 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0910

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.918 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: 0.811 AC: 123291 AN: 152060 Hom.: 50595 Cov.: 32

Gnomad AFR AF: 0.926

Gnomad AMI AF: 0.696

Gnomad AMR AF: 0.830

Gnomad ASJ AF: 0.747

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.926

Gnomad FIN AF: 0.763

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.731

Gnomad OTH AF: 0.799

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

GnomAD4 genome AF: 0.811 AC: 123390 AN: 152178 Hom.: 50636 Cov.: 32 AF XY: 0.816 AC XY: 60717 AN XY: 74370

Gnomad4 AFR AF: 0.926

Gnomad4 AMR AF: 0.830

Gnomad4 ASJ AF: 0.747

Gnomad4 EAS AF: 0.937

Gnomad4 SAS AF: 0.925

Gnomad4 FIN AF: 0.763

Gnomad4 NFE AF: 0.731

Gnomad4 OTH AF: 0.801

Alfa AF: 0.748 Hom.: 84540

Bravo AF: 0.819

Asia WGS AF: 0.941 AC: 3273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3923229; hg19: chr2-85562172;