chr1-212920692-G-A

Variant names:

• chr1-212920692-G-A
• rs1284864

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.801 AC: 33225 AN: 41460

American (AMR) AF: 0.930 AC: 14221 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.888 AC: 3080 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5148 AN: 5152

South Asian (SAS) AF: 0.897 AC: 4327 AN: 4824

European-Finnish (FIN) AF: 0.931 AC: 9865 AN: 10598

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.898 AC: 61056 AN: 67976

Other (OTH) AF: 0.908 AC: 1907 AN: 2100

Alfa AF: 0.896 Hom.: 71571

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
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1284864; hg19: chr1-213094034;