chr1-197854230-A-G

Variant names:

• chr1-197854230-A-G
• rs10922306

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 0.69 in 151,978 control chromosomes in the GnomAD database, including 36,775 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 0.69 (36775 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.630
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.823 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: 0.690 AC: 104800 AN: 151860 Hom.: 36753 Cov.: 31

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.774

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.831

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.690 AC: 104873 AN: 151978 Hom.: 36775 Cov.: 31 AF XY: 0.698 AC XY: 51879 AN XY: 74282

African (AFR) AF: 0.581 AC: 24077 AN: 41432

American (AMR) AF: 0.775 AC: 11828 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.735 AC: 2547 AN: 3466

East Asian (EAS) AF: 0.831 AC: 4299 AN: 5172

South Asian (SAS) AF: 0.845 AC: 4071 AN: 4820

European-Finnish (FIN) AF: 0.735 AC: 7759 AN: 10552

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.709 AC: 48177 AN: 67962

Other (OTH) AF: 0.732 AC: 1542 AN: 2106

Alfa AF: 0.704 Hom.: 120062

Bravo AF: 0.684

Asia WGS AF: 0.841 AC: 2914 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.2
DANN	Benign	0.55
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs10922306; hg19: chr1-197823360;