1-206767486-A-G

Position:

• chr1-206767486-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 0.42 in 151,946 control chromosomes in the GnomAD database, including 14,099 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 0.42 (14099 hom., cov: 31)
  • Exomes 𝑓: 0.49 (24 hom.)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.405

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.206767486A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63732 AN: 151828 Hom.: 14078 Cov.: 31

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.0521

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.395

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.489 AC: 93 AN: 190 Hom.: 24 AF XY: 0.491 AC XY: 56 AN XY: 114

Gnomad4 AFR exome AF: 0.750

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 0.397

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.717

GnomAD4 genome AF: 0.420 AC: 63801 AN: 151946 Hom.: 14099 Cov.: 31 AF XY: 0.412 AC XY: 30603 AN XY: 74250

Gnomad4 AFR AF: 0.406

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.408

Gnomad4 EAS AF: 0.0520

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.472

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.397

Alfa AF: 0.400 Hom.: 2498

Bravo AF: 0.409

Asia WGS AF: 0.196 AC: 681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.7
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3024500; hg19: chr1-206940831;