1-200533543-A-G

Variant names:

• chr1-200533543-A-G
• rs10919967

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.891 AC: 36926 AN: 41466

American (AMR) AF: 0.739 AC: 11262 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.895 AC: 3106 AN: 3472

East Asian (EAS) AF: 0.731 AC: 3783 AN: 5172

South Asian (SAS) AF: 0.784 AC: 3764 AN: 4804

European-Finnish (FIN) AF: 0.815 AC: 8614 AN: 10564

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.818 AC: 55621 AN: 68004

Other (OTH) AF: 0.825 AC: 1739 AN: 2108

Alfa AF: 0.813 Hom.: 95950

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
PhyloP100		0.078

Splicing

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

Other links and lift over

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