rs3093068

chr1-159711574-G-C

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 0.126 in 152,240 control chromosomes in the GnomAD database, including 1,816 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 0.13 (1816 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.236

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.264 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: 0.126 AC: 19147 AN: 152122 Hom.: 1818 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0750

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.0659

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0610

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.126 AC: 19162 AN: 152240 Hom.: 1816 Cov.: 32 AF XY: 0.124 AC XY: 9202 AN XY: 74422

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.0748

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.0659

Gnomad4 NFE AF: 0.0610

Gnomad4 OTH AF: 0.123

Alfa AF: 0.0948 Hom.: 173

Bravo AF: 0.132

Asia WGS AF: 0.105 AC: 365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.47
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3093068; hg19: chr1-159681364;