rs1435883

Variant names:

• chr2-81415381-A-G
• rs1435883

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;