rs1429412

Variant names:

• chr2-197326170-A-G
• rs1429412

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 16 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.374 AC: 15501 AN: 41466

American (AMR) AF: 0.391 AC: 5971 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 936 AN: 3466

East Asian (EAS) AF: 0.476 AC: 2447 AN: 5144

South Asian (SAS) AF: 0.306 AC: 1477 AN: 4824

European-Finnish (FIN) AF: 0.450 AC: 4752 AN: 10560

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.335 AC: 22782 AN: 67938

Other (OTH) AF: 0.329 AC: 694 AN: 2112

Alfa AF: 0.344 Hom.: 7378

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
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs1429412; hg19: chr2-198190894;