chr1-209817204-C-T

Variant names:

• chr1-209817204-C-T
• rs658860

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 0.825 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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.870 AC: 36094 AN: 41468

American (AMR) AF: 0.838 AC: 12812 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.812 AC: 2815 AN: 3468

East Asian (EAS) AF: 0.808 AC: 4101 AN: 5074

South Asian (SAS) AF: 0.780 AC: 3755 AN: 4814

European-Finnish (FIN) AF: 0.777 AC: 8212 AN: 10568

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.807 AC: 54854 AN: 67970

Other (OTH) AF: 0.830 AC: 1753 AN: 2112

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
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs658860; hg19: chr1-209990549;