1-209817204-C-T

Position:

• chr1-209817204-C-T

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 0.825 in 151,962 control chromosomes in the GnomAD database, including 51,840 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 (51840 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75

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 = 0.863 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: 0.825 AC: 125341 AN: 151844 Hom.: 51810 Cov.: 30

Gnomad AFR AF: 0.871

Gnomad AMI AF: 0.864

Gnomad AMR AF: 0.839

Gnomad ASJ AF: 0.812

Gnomad EAS AF: 0.808

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.777

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.807

Gnomad OTH AF: 0.833

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

GnomAD4 genome AF: 0.825 AC: 125426 AN: 151962 Hom.: 51840 Cov.: 30 AF XY: 0.823 AC XY: 61087 AN XY: 74256

Gnomad4 AFR AF: 0.870

Gnomad4 AMR AF: 0.838

Gnomad4 ASJ AF: 0.812

Gnomad4 EAS AF: 0.808

Gnomad4 SAS AF: 0.780

Gnomad4 FIN AF: 0.777

Gnomad4 NFE AF: 0.807

Gnomad4 OTH AF: 0.830

Alfa AF: 0.815 Hom.: 6258

Bravo AF: 0.830

Asia WGS AF: 0.761 AC: 2648 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	0.037
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs658860; hg19: chr1-209990549;