rs807061

Variant names:

• chr1-25916391-G-A
• rs807061

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 0.635 in 152,006 control chromosomes in the GnomAD database, including 33,093 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 0.63 (33093 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.294

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.635 AC: 96442 AN: 151888 Hom.: 33075 Cov.: 32

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.752

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.694

Gnomad SAS AF: 0.842

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.750

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.635 AC: 96489 AN: 152006 Hom.: 33093 Cov.: 32 AF XY: 0.639 AC XY: 47463 AN XY: 74276

Gnomad4 AFR AF: 0.350

Gnomad4 AMR AF: 0.733

Gnomad4 ASJ AF: 0.663

Gnomad4 EAS AF: 0.693

Gnomad4 SAS AF: 0.843

Gnomad4 FIN AF: 0.722

Gnomad4 NFE AF: 0.750

Gnomad4 OTH AF: 0.646

Alfa AF: 0.721 Hom.: 67779

Bravo AF: 0.613

Asia WGS AF: 0.767 AC: 2668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	11
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs807061; hg19: chr1-26242882;