1-162044842-A-G

Variant names:

• chr1-162044842-A-G
• rs2880058

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 0.479 in 152,026 control chromosomes in the GnomAD database, including 19,849 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 (19849 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.548
• Publications: 35 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.718 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: 0.479 AC: 72787 AN: 151908 Hom.: 19818 Cov.: 31

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.479 AC: 72858 AN: 152026 Hom.: 19849 Cov.: 31 AF XY: 0.482 AC XY: 35809 AN XY: 74328

African (AFR) AF: 0.724 AC: 30048 AN: 41476

American (AMR) AF: 0.414 AC: 6324 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1348 AN: 3470

East Asian (EAS) AF: 0.712 AC: 3681 AN: 5172

South Asian (SAS) AF: 0.651 AC: 3132 AN: 4810

European-Finnish (FIN) AF: 0.363 AC: 3834 AN: 10554

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.339 AC: 23052 AN: 67952

Other (OTH) AF: 0.459 AC: 970 AN: 2112

Alfa AF: 0.376 Hom.: 51205

Bravo AF: 0.487

Asia WGS AF: 0.683 AC: 2374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.47
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs2880058; hg19: chr1-162014632;