1-200533543-A-G

Position:

• chr1-200533543-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 0.827 in 152,038 control chromosomes in the GnomAD database, including 52,217 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 0.83 (52217 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.883 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.827 AC: 125600 AN: 151922 Hom.: 52187 Cov.: 30

Gnomad AFR AF: 0.890

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.895

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.785

Gnomad FIN AF: 0.815

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.826

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

GnomAD4 genome AF: 0.827 AC: 125684 AN: 152038 Hom.: 52217 Cov.: 30 AF XY: 0.823 AC XY: 61197 AN XY: 74322

Gnomad4 AFR AF: 0.891

Gnomad4 AMR AF: 0.739

Gnomad4 ASJ AF: 0.895

Gnomad4 EAS AF: 0.731

Gnomad4 SAS AF: 0.784

Gnomad4 FIN AF: 0.815

Gnomad4 NFE AF: 0.818

Gnomad4 OTH AF: 0.825

Alfa AF: 0.812 Hom.: 73406

Bravo AF: 0.820

Asia WGS AF: 0.777 AC: 2703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.0
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10919967; hg19: chr1-200502671; COSMIC: COSV60017781;