chr1-159312221-A-G

Variant names:

• chr1-159312221-A-G
• rs2427829

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 0.797 in 152,170 control chromosomes in the GnomAD database, including 49,121 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 0.80 (49121 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.430
• Publications: 4 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 = 0.935 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.797 AC: 121179 AN: 152052 Hom.: 49070 Cov.: 32

Gnomad AFR AF: 0.942

Gnomad AMI AF: 0.771

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.943

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.737

Gnomad OTH AF: 0.786

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

GnomAD4 genome AF: 0.797 AC: 121287 AN: 152170 Hom.: 49121 Cov.: 32 AF XY: 0.791 AC XY: 58832 AN XY: 74372

African (AFR) AF: 0.942 AC: 39161 AN: 41556

American (AMR) AF: 0.758 AC: 11594 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.709 AC: 2456 AN: 3466

East Asian (EAS) AF: 0.943 AC: 4885 AN: 5178

South Asian (SAS) AF: 0.629 AC: 3023 AN: 4808

European-Finnish (FIN) AF: 0.708 AC: 7484 AN: 10566

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.737 AC: 50108 AN: 67986

Other (OTH) AF: 0.785 AC: 1661 AN: 2116

Alfa AF: 0.753 Hom.: 55060

Bravo AF: 0.813

Asia WGS AF: 0.775 AC: 2696 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.63
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs2427829; hg19: chr1-159282011;