rs1420094

Variant names:

• chr2-102399227-C-T
• rs1420094

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 0.535 in 152,080 control chromosomes in the GnomAD database, including 23,625 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 0.53 (23625 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.958

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.726 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: 0.535 AC: 81272 AN: 151962 Hom.: 23594 Cov.: 33

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.535 AC: 81356 AN: 152080 Hom.: 23625 Cov.: 33 AF XY: 0.529 AC XY: 39323 AN XY: 74354

Gnomad4 AFR AF: 0.733

Gnomad4 AMR AF: 0.414

Gnomad4 ASJ AF: 0.614

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.543

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.520

Alfa AF: 0.484 Hom.: 8605

Bravo AF: 0.536

Asia WGS AF: 0.232 AC: 809 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.64
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1420094; hg19: chr2-103015687; COSMIC: COSV52123631;