rs11894053

Positions:

• chr2-42002405-A-G

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 0.257 in 152,180 control chromosomes in the GnomAD database, including 5,392 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 0.26 (5392 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.109

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.318 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: 0.257 AC: 39125 AN: 152062 Hom.: 5388 Cov.: 33

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.257 AC: 39158 AN: 152180 Hom.: 5392 Cov.: 33 AF XY: 0.260 AC XY: 19347 AN XY: 74414

Gnomad4 AFR AF: 0.323

Gnomad4 AMR AF: 0.187

Gnomad4 ASJ AF: 0.321

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.229

Gnomad4 OTH AF: 0.265

Alfa AF: 0.234 Hom.: 733

Bravo AF: 0.251

Asia WGS AF: 0.205 AC: 716 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	3.4
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11894053; hg19: chr2-42229545;