rs927724

Variant names:

• chr1-196205660-G-A
• rs927724

Your query was ambiguous. Multiple possible variants found:

• chr1-196205660-G-A
• chr1-196205660-G-T

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 0.893 in 152,096 control chromosomes in the GnomAD database, including 60,756 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 (60756 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.903 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: 0.893 AC: 135770 AN: 151982 Hom.: 60688 Cov.: 31

Gnomad AFR AF: 0.910

Gnomad AMI AF: 0.948

Gnomad AMR AF: 0.910

Gnomad ASJ AF: 0.866

Gnomad EAS AF: 0.876

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.902

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.883

Gnomad OTH AF: 0.900

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

GnomAD4 genome AF: 0.893 AC: 135894 AN: 152096 Hom.: 60756 Cov.: 31 AF XY: 0.893 AC XY: 66421 AN XY: 74354

African (AFR) AF: 0.910 AC: 37788 AN: 41506

American (AMR) AF: 0.910 AC: 13906 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.866 AC: 3006 AN: 3472

East Asian (EAS) AF: 0.876 AC: 4527 AN: 5170

South Asian (SAS) AF: 0.861 AC: 4152 AN: 4822

European-Finnish (FIN) AF: 0.902 AC: 9503 AN: 10538

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.883 AC: 60004 AN: 67990

Other (OTH) AF: 0.901 AC: 1902 AN: 2110

Alfa AF: 0.885 Hom.: 84937

Bravo AF: 0.897

Asia WGS AF: 0.874 AC: 3024 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.51
DANN	Benign	0.24
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs927724; hg19: chr1-196174790;