rs1418029

Variant names:

• chr20-2079505-G-A
• rs1418029

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 0.228 in 152,122 control chromosomes in the GnomAD database, including 7,021 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 0.23 (7021 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.610

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.804 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: 0.228 AC: 34627 AN: 152004 Hom.: 7004 Cov.: 32

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.0579

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0626

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.228 AC: 34680 AN: 152122 Hom.: 7021 Cov.: 32 AF XY: 0.240 AC XY: 17808 AN XY: 74348

Gnomad4 AFR AF: 0.414

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.0579

Gnomad4 EAS AF: 0.825

Gnomad4 SAS AF: 0.413

Gnomad4 FIN AF: 0.129

Gnomad4 NFE AF: 0.0626

Gnomad4 OTH AF: 0.196

Alfa AF: 0.167 Hom.: 1108

Bravo AF: 0.254

Asia WGS AF: 0.616 AC: 2141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	3.3
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1418029; hg19: chr20-2060151; COSMIC: COSV69900898;