chr1-162068066-A-G

Position:

• chr1-162068066-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 0.359 in 152,066 control chromosomes in the GnomAD database, including 10,341 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 0.36 (10341 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.162068066A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54479 AN: 151948 Hom.: 10326 Cov.: 32

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.359 AC: 54529 AN: 152066 Hom.: 10341 Cov.: 32 AF XY: 0.365 AC XY: 27143 AN XY: 74326

Gnomad4 AFR AF: 0.428

Gnomad4 AMR AF: 0.339

Gnomad4 ASJ AF: 0.327

Gnomad4 EAS AF: 0.533

Gnomad4 SAS AF: 0.629

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.349

Alfa AF: 0.309 Hom.: 7413

Bravo AF: 0.352

Asia WGS AF: 0.583 AC: 2026 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	8.4
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10753746; hg19: chr1-162037856;