rs2420134

Variant names:

• chr1-169504523-G-A
• rs2420134

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 0.0568 in 152,198 control chromosomes in the GnomAD database, including 368 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 0.057 (368 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.250

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.097 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: 0.0568 AC: 8631 AN: 152080 Hom.: 367 Cov.: 32

Gnomad AFR AF: 0.0170

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0749

Gnomad EAS AF: 0.0296

Gnomad SAS AF: 0.0657

Gnomad FIN AF: 0.0862

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0673

Gnomad OTH AF: 0.0642

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

GnomAD4 genome AF: 0.0568 AC: 8640 AN: 152198 Hom.: 368 Cov.: 32 AF XY: 0.0590 AC XY: 4390 AN XY: 74418

Gnomad4 AFR AF: 0.0171

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.0749

Gnomad4 EAS AF: 0.0297

Gnomad4 SAS AF: 0.0655

Gnomad4 FIN AF: 0.0862

Gnomad4 NFE AF: 0.0674

Gnomad4 OTH AF: 0.0635

Alfa AF: 0.0671 Hom.: 378

Bravo AF: 0.0529

Asia WGS AF: 0.0580 AC: 202 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.6
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2420134; hg19: chr1-169473761;