rs1284864

Variant names:

• chr1-212920692-G-A
• rs1284864

Your query was ambiguous. Multiple possible variants found:

• chr1-212920692-G-A
• chr1-212920692-G-C

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 0.881 in 152,072 control chromosomes in the GnomAD database, including 59,188 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 0.88 (59188 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42

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 (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.881 AC: 133867 AN: 151954 Hom.: 59143 Cov.: 29

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.966

Gnomad AMR AF: 0.930

Gnomad ASJ AF: 0.888

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.896

Gnomad FIN AF: 0.931

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.898

Gnomad OTH AF: 0.909

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

GnomAD4 genome AF: 0.881 AC: 133970 AN: 152072 Hom.: 59188 Cov.: 29 AF XY: 0.885 AC XY: 65771 AN XY: 74358

Gnomad4 AFR AF: 0.801

Gnomad4 AMR AF: 0.930

Gnomad4 ASJ AF: 0.888

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.897

Gnomad4 FIN AF: 0.931

Gnomad4 NFE AF: 0.898

Gnomad4 OTH AF: 0.908

Alfa AF: 0.899 Hom.: 56223

Bravo AF: 0.879

Asia WGS AF: 0.938 AC: 3262 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	0.36
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1284864; hg19: chr1-213094034;