1-17876886-C-G

Variant names:

• chr1-17876886-C-G
• rs578987

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.322

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;