rs7250581

Variant names:

• chr19-29573489-A-G
• rs7250581

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 0.888 in 152,226 control chromosomes in the GnomAD database, including 60,375 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 0.89 (60375 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.888 AC: 135045 AN: 152108 Hom.: 60319 Cov.: 32

Gnomad AFR AF: 0.967

Gnomad AMI AF: 0.898

Gnomad AMR AF: 0.913

Gnomad ASJ AF: 0.948

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.978

Gnomad FIN AF: 0.857

Gnomad MID AF: 0.984

Gnomad NFE AF: 0.820

Gnomad OTH AF: 0.903

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

GnomAD4 genome AF: 0.888 AC: 135159 AN: 152226 Hom.: 60375 Cov.: 32 AF XY: 0.893 AC XY: 66450 AN XY: 74416

African (AFR) AF: 0.967 AC: 40184 AN: 41542

American (AMR) AF: 0.913 AC: 13960 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.948 AC: 3293 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5181 AN: 5188

South Asian (SAS) AF: 0.977 AC: 4711 AN: 4820

European-Finnish (FIN) AF: 0.857 AC: 9080 AN: 10590

Middle Eastern (MID) AF: 0.976 AC: 287 AN: 294

European-Non Finnish (NFE) AF: 0.820 AC: 55732 AN: 68002

Other (OTH) AF: 0.904 AC: 1912 AN: 2114

Alfa AF: 0.851 Hom.: 72541

Bravo AF: 0.894

Asia WGS AF: 0.985 AC: 3425 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	0.91
DANN	Benign	0.16
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs7250581; hg19: chr19-30064396;