1-186537480-G-A

Position:

• chr1-186537480-G-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 0.345 in 151,834 control chromosomes in the GnomAD database, including 10,007 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 0.34 (10007 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.639

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.504 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52212 AN: 151716 Hom.: 9962 Cov.: 32

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.345 AC: 52307 AN: 151834 Hom.: 10007 Cov.: 32 AF XY: 0.344 AC XY: 25524 AN XY: 74224

Gnomad4 AFR AF: 0.510

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.423

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.359

Alfa AF: 0.315 Hom.: 1742

Bravo AF: 0.370

Asia WGS AF: 0.399 AC: 1384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
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: rs10911877; hg19: chr1-186506612;