1-21495264-A-G

Variant names:

• chr1-21495264-A-G
• rs1780324

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 0.484 in 152,002 control chromosomes in the GnomAD database, including 19,086 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 0.48 (19086 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.772
• Publications: 44 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73515 AN: 151884 Hom.: 19090 Cov.: 31

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.703

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.484 AC: 73511 AN: 152002 Hom.: 19086 Cov.: 31 AF XY: 0.487 AC XY: 36204 AN XY: 74302

African (AFR) AF: 0.281 AC: 11654 AN: 41438

American (AMR) AF: 0.570 AC: 8709 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.568 AC: 1965 AN: 3460

East Asian (EAS) AF: 0.703 AC: 3638 AN: 5176

South Asian (SAS) AF: 0.514 AC: 2468 AN: 4802

European-Finnish (FIN) AF: 0.529 AC: 5591 AN: 10574

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.556 AC: 37789 AN: 67958

Other (OTH) AF: 0.526 AC: 1109 AN: 2108

Alfa AF: 0.537 Hom.: 109151

Bravo AF: 0.477

Asia WGS AF: 0.547 AC: 1902 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.49
DANN	Benign	0.73
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs1780324; hg19: chr1-21821757;