1-200533543-A-G

Variant names:

• chr1-200533543-A-G
• rs10919967

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;