chr2-53464911-G-C

Position:

• chr2-53464911-G-C

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 0.169 in 152,156 control chromosomes in the GnomAD database, including 3,338 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 0.17 (3338 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0370

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.351 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: 0.168 AC: 25587 AN: 152038 Hom.: 3313 Cov.: 32

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.0909

Gnomad SAS AF: 0.0855

Gnomad FIN AF: 0.0466

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.0806

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.169 AC: 25669 AN: 152156 Hom.: 3338 Cov.: 32 AF XY: 0.166 AC XY: 12355 AN XY: 74382

Gnomad4 AFR AF: 0.356

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.0907

Gnomad4 SAS AF: 0.0866

Gnomad4 FIN AF: 0.0466

Gnomad4 NFE AF: 0.0806

Gnomad4 OTH AF: 0.176

Alfa AF: 0.132 Hom.: 264

Bravo AF: 0.189

Asia WGS AF: 0.106 AC: 371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.91
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs903228; hg19: chr2-53692049;