chr1-206766559-G-A

Position:

• chr1-206766559-G-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 0.112 in 152,218 control chromosomes in the GnomAD database, including 1,196 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 0.11 (1196 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.244

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17116 AN: 152098 Hom.: 1196 Cov.: 33

Gnomad AFR AF: 0.0461

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.0816

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.0254

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.112 AC: 17110 AN: 152218 Hom.: 1196 Cov.: 33 AF XY: 0.111 AC XY: 8243 AN XY: 74408

Gnomad4 AFR AF: 0.0461

Gnomad4 AMR AF: 0.0814

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.0251

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.122

Alfa AF: 0.144 Hom.: 3275

Bravo AF: 0.103

Asia WGS AF: 0.0570 AC: 198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.8
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3024505; hg19: chr1-206939904;