rs1429412

Variant names:

• chr2-197326170-A-G
• rs1429412

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 0.361 in 151,984 control chromosomes in the GnomAD database, including 10,181 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 0.36 (10181 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.492

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 (EAS) allele frequency at 95% confidence interval = 0.46 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: 0.361 AC: 54818 AN: 151864 Hom.: 10160 Cov.: 31

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.361 AC: 54876 AN: 151984 Hom.: 10181 Cov.: 31 AF XY: 0.363 AC XY: 26971 AN XY: 74268

Gnomad4 AFR AF: 0.374

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.476

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.450

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.329

Alfa AF: 0.344 Hom.: 6233

Bravo AF: 0.362

Asia WGS AF: 0.402 AC: 1395 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	2.6
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1429412; hg19: chr2-198190894;