chr1-37078622-A-G

Variant names:

• chr1-37078622-A-G
• rs218428

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 0.811 in 152,132 control chromosomes in the GnomAD database, including 50,774 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 0.81 (50774 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.75
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.899 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: 0.811 AC: 123258 AN: 152016 Hom.: 50719 Cov.: 31

Gnomad AFR AF: 0.906

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.848

Gnomad ASJ AF: 0.824

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.743

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.828

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

GnomAD4 genome AF: 0.811 AC: 123373 AN: 152132 Hom.: 50774 Cov.: 31 AF XY: 0.805 AC XY: 59865 AN XY: 74386

African (AFR) AF: 0.906 AC: 37619 AN: 41510

American (AMR) AF: 0.848 AC: 12969 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.824 AC: 2862 AN: 3472

East Asian (EAS) AF: 0.407 AC: 2104 AN: 5164

South Asian (SAS) AF: 0.752 AC: 3617 AN: 4810

European-Finnish (FIN) AF: 0.743 AC: 7867 AN: 10594

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.790 AC: 53707 AN: 67966

Other (OTH) AF: 0.825 AC: 1740 AN: 2108

Alfa AF: 0.800 Hom.: 109033

Bravo AF: 0.821

Asia WGS AF: 0.634 AC: 2205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	17
DANN	Benign	0.68
PhyloP100		2.8

Splicing

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

Other links and lift over

dbSNP: rs218428; hg19: chr1-37544223;