rs1449263

chr2-181454574-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 0.555 in 151,978 control chromosomes in the GnomAD database, including 23,741 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 0.55 (23741 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.582 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: 0.555 AC: 84280 AN: 151860 Hom.: 23722 Cov.: 31

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.555 AC: 84343 AN: 151978 Hom.: 23741 Cov.: 31 AF XY: 0.558 AC XY: 41458 AN XY: 74294

Gnomad4 AFR AF: 0.583

Gnomad4 AMR AF: 0.543

Gnomad4 ASJ AF: 0.489

Gnomad4 EAS AF: 0.362

Gnomad4 SAS AF: 0.600

Gnomad4 FIN AF: 0.610

Gnomad4 NFE AF: 0.547

Gnomad4 OTH AF: 0.546

Alfa AF: 0.552 Hom.: 2268

Bravo AF: 0.550

Asia WGS AF: 0.481 AC: 1675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.4
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1449263; hg19: chr2-182319301;