chr1-187927074-C-A

Position:

• chr1-187927074-C-A

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 0.782 in 152,070 control chromosomes in the GnomAD database, including 46,825 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 0.78 (46825 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.339

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.187927074C>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.781 AC: 118739 AN: 151952 Hom.: 46780 Cov.: 32

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.855

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.805

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.787

Gnomad OTH AF: 0.790

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

GnomAD4 genome AF: 0.782 AC: 118846 AN: 152070 Hom.: 46825 Cov.: 32 AF XY: 0.778 AC XY: 57788 AN XY: 74320

Gnomad4 AFR AF: 0.835

Gnomad4 AMR AF: 0.712

Gnomad4 ASJ AF: 0.805

Gnomad4 EAS AF: 0.512

Gnomad4 SAS AF: 0.761

Gnomad4 FIN AF: 0.760

Gnomad4 NFE AF: 0.787

Gnomad4 OTH AF: 0.793

Alfa AF: 0.776 Hom.: 7235

Bravo AF: 0.777

Asia WGS AF: 0.665 AC: 2311 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.77
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs666282; hg19: chr1-187896205;