1-200715929-G-A

Variant names:

• chr1-200715929-G-A
• rs7519783

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 0.695 in 152,048 control chromosomes in the GnomAD database, including 36,988 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 (36988 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.728 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.695 AC: 105616 AN: 151930 Hom.: 36980 Cov.: 32

Gnomad AFR AF: 0.616

Gnomad AMI AF: 0.835

Gnomad AMR AF: 0.739

Gnomad ASJ AF: 0.723

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.707

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.695 AC: 105664 AN: 152048 Hom.: 36988 Cov.: 32 AF XY: 0.696 AC XY: 51714 AN XY: 74304

African (AFR) AF: 0.616 AC: 25517 AN: 41448

American (AMR) AF: 0.739 AC: 11292 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.723 AC: 2511 AN: 3472

East Asian (EAS) AF: 0.739 AC: 3826 AN: 5180

South Asian (SAS) AF: 0.706 AC: 3401 AN: 4816

European-Finnish (FIN) AF: 0.693 AC: 7318 AN: 10554

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.725 AC: 49308 AN: 67990

Other (OTH) AF: 0.718 AC: 1513 AN: 2108

Alfa AF: 0.713 Hom.: 22734

Bravo AF: 0.695

Asia WGS AF: 0.714 AC: 2487 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.5
DANN	Benign	0.17
PhyloP100		0.041

Splicing

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

Other links and lift over

dbSNP: rs7519783; hg19: chr1-200685057;