chr1-17876886-C-G

Position:

• chr1-17876886-C-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 0.734 in 151,790 control chromosomes in the GnomAD database, including 41,152 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 0.73 (41152 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.322

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.863 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.17876886C>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.734 AC: 111319 AN: 151672 Hom.: 41112 Cov.: 30

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.734

Gnomad FIN AF: 0.763

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.699

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

GnomAD4 genome AF: 0.734 AC: 111424 AN: 151790 Hom.: 41152 Cov.: 30 AF XY: 0.735 AC XY: 54527 AN XY: 74160

Gnomad4 AFR AF: 0.793

Gnomad4 AMR AF: 0.728

Gnomad4 ASJ AF: 0.609

Gnomad4 EAS AF: 0.885

Gnomad4 SAS AF: 0.734

Gnomad4 FIN AF: 0.763

Gnomad4 NFE AF: 0.694

Gnomad4 OTH AF: 0.702

Alfa AF: 0.645 Hom.: 2122

Bravo AF: 0.735

Asia WGS AF: 0.808 AC: 2812 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.10
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs578987; hg19: chr1-18203380; COSMIC: COSV59928138;