rs1260333

chr2-27525757-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 0.58 in 142,650 control chromosomes in the GnomAD database, including 24,634 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 0.58 (24634 hom., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.420

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 (SAS) allele frequency at 95% confidence interval = 0.688 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: 0.580 AC: 82643 AN: 142604 Hom.: 24603 Cov.: 22

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.708

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.580 AC: 82709 AN: 142650 Hom.: 24634 Cov.: 22 AF XY: 0.581 AC XY: 39942 AN XY: 68722

Gnomad4 AFR AF: 0.665

Gnomad4 AMR AF: 0.559

Gnomad4 ASJ AF: 0.437

Gnomad4 EAS AF: 0.500

Gnomad4 SAS AF: 0.709

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.544

Gnomad4 OTH AF: 0.523

Alfa AF: 0.558 Hom.: 17679

Bravo AF: 0.581

Asia WGS AF: 0.630 AC: 2012 AN: 3200

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	4.6
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1260333; hg19: chr2-27748624;