1-159766965-A-G

Position:

• chr1-159766965-A-G

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 0.16 in 152,244 control chromosomes in the GnomAD database, including 2,372 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 0.16 (2372 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.370

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.159766965A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24408 AN: 152126 Hom.: 2369 Cov.: 33

Gnomad AFR AF: 0.0705

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.160 AC: 24415 AN: 152244 Hom.: 2372 Cov.: 33 AF XY: 0.168 AC XY: 12521 AN XY: 74434

Gnomad4 AFR AF: 0.0702

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.122

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.327

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.129

Alfa AF: 0.168 Hom.: 2372

Bravo AF: 0.150

Asia WGS AF: 0.122 AC: 424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.6
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4364879; hg19: chr1-159736755;