1-202086810-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 0.772 in 152,192 control chromosomes in the GnomAD database, including 45,942 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 0.77 (45942 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

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 (AFR) allele frequency at 95% confidence interval = 0.885 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: 0.772 AC: 117448 AN: 152074 Hom.: 45899 Cov.: 32

Gnomad AFR AF: 0.893

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.812

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.781

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.763

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

GnomAD4 genome AF: 0.772 AC: 117541 AN: 152192 Hom.: 45942 Cov.: 32 AF XY: 0.775 AC XY: 57662 AN XY: 74388

Gnomad4 AFR AF: 0.893

Gnomad4 AMR AF: 0.812

Gnomad4 ASJ AF: 0.770

Gnomad4 EAS AF: 0.667

Gnomad4 SAS AF: 0.780

Gnomad4 FIN AF: 0.714

Gnomad4 NFE AF: 0.709

Gnomad4 OTH AF: 0.759

Alfa AF: 0.728 Hom.: 57098

Bravo AF: 0.783

Asia WGS AF: 0.721 AC: 2511 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	0.25
Dann	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10800812; hg19: chr1-202055938;