rs6604025

Variant names:

• chr1-92819609-C-A
• rs6604025

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 0.858 in 152,126 control chromosomes in the GnomAD database, including 56,410 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 0.86 (56410 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.938 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: 0.858 AC: 130456 AN: 152008 Hom.: 56387 Cov.: 30

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.955

Gnomad AMR AF: 0.898

Gnomad ASJ AF: 0.953

Gnomad EAS AF: 0.960

Gnomad SAS AF: 0.927

Gnomad FIN AF: 0.883

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.894

Gnomad OTH AF: 0.851

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

GnomAD4 genome AF: 0.858 AC: 130535 AN: 152126 Hom.: 56410 Cov.: 30 AF XY: 0.861 AC XY: 64013 AN XY: 74364

African (AFR) AF: 0.748 AC: 31009 AN: 41452

American (AMR) AF: 0.898 AC: 13724 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.953 AC: 3308 AN: 3470

East Asian (EAS) AF: 0.960 AC: 4969 AN: 5174

South Asian (SAS) AF: 0.928 AC: 4465 AN: 4814

European-Finnish (FIN) AF: 0.883 AC: 9352 AN: 10594

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.894 AC: 60782 AN: 68018

Other (OTH) AF: 0.851 AC: 1798 AN: 2114

Alfa AF: 0.875 Hom.: 7262

Bravo AF: 0.852

Asia WGS AF: 0.902 AC: 3140 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	0.37
DANN	Benign	0.48
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs6604025; hg19: chr1-93285166;