rs6604025

chr1-92819609-C-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.748

Gnomad4 AMR AF: 0.898

Gnomad4 ASJ AF: 0.953

Gnomad4 EAS AF: 0.960

Gnomad4 SAS AF: 0.928

Gnomad4 FIN AF: 0.883

Gnomad4 NFE AF: 0.894

Gnomad4 OTH AF: 0.851

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.37
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6604025; hg19: chr1-93285166;