rs1869051

Positions:

• chr2-133686449-G-A
• chr2-133686449-G-T

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 0.644 in 152,002 control chromosomes in the GnomAD database, including 31,931 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 0.64 (31931 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.498

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.644 AC: 97835 AN: 151884 Hom.: 31870 Cov.: 32

Gnomad AFR AF: 0.707

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.644 AC: 97956 AN: 152002 Hom.: 31931 Cov.: 32 AF XY: 0.644 AC XY: 47838 AN XY: 74288

Gnomad4 AFR AF: 0.708

Gnomad4 AMR AF: 0.606

Gnomad4 ASJ AF: 0.629

Gnomad4 EAS AF: 0.749

Gnomad4 SAS AF: 0.609

Gnomad4 FIN AF: 0.627

Gnomad4 NFE AF: 0.615

Gnomad4 OTH AF: 0.644

Alfa AF: 0.625 Hom.: 10525

Bravo AF: 0.648

Asia WGS AF: 0.688 AC: 2392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.15
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1869051; hg19: chr2-134444020; COSMIC: COSV65107417;