rs1435883

Positions:

• chr2-81415381-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 0.38 in 151,982 control chromosomes in the GnomAD database, including 12,675 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 0.38 (12675 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.691

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57673 AN: 151864 Hom.: 12631 Cov.: 32

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.380 AC: 57768 AN: 151982 Hom.: 12675 Cov.: 32 AF XY: 0.369 AC XY: 27405 AN XY: 74298

Gnomad4 AFR AF: 0.608

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.291

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.302

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.314

Alfa AF: 0.324 Hom.: 16932

Bravo AF: 0.387

Asia WGS AF: 0.156 AC: 543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.25
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1435883; hg19: chr2-81642505;