1-162891123-A-G

Position:

• chr1-162891123-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 0.774 in 152,102 control chromosomes in the GnomAD database, including 47,788 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 0.77 (47788 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.232

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.162891123A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.774 AC: 117616 AN: 151984 Hom.: 47787 Cov.: 31

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.894

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.734

Gnomad FIN AF: 0.928

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.911

Gnomad OTH AF: 0.799

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

GnomAD4 genome AF: 0.774 AC: 117666 AN: 152102 Hom.: 47788 Cov.: 31 AF XY: 0.771 AC XY: 57296 AN XY: 74354

Gnomad4 AFR AF: 0.549

Gnomad4 AMR AF: 0.760

Gnomad4 ASJ AF: 0.894

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.734

Gnomad4 FIN AF: 0.928

Gnomad4 NFE AF: 0.911

Gnomad4 OTH AF: 0.798

Alfa AF: 0.886 Hom.: 75674

Bravo AF: 0.750

Asia WGS AF: 0.551 AC: 1913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.95
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4412572; hg19: chr1-162860913;