1-203199346-A-T

Variant names:

• chr1-203199346-A-T
• rs2153101

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 0.843 in 152,322 control chromosomes in the GnomAD database, including 54,494 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 0.84 (54494 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.225
• Publications: 18 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.921 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.843 AC: 128330 AN: 152206 Hom.: 54446 Cov.: 34

Gnomad AFR AF: 0.929

Gnomad AMI AF: 0.916

Gnomad AMR AF: 0.880

Gnomad ASJ AF: 0.898

Gnomad EAS AF: 0.927

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.741

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.853

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

GnomAD4 genome AF: 0.843 AC: 128438 AN: 152322 Hom.: 54494 Cov.: 34 AF XY: 0.843 AC XY: 62778 AN XY: 74476

African (AFR) AF: 0.929 AC: 38609 AN: 41580

American (AMR) AF: 0.880 AC: 13465 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.898 AC: 3118 AN: 3472

East Asian (EAS) AF: 0.927 AC: 4802 AN: 5182

South Asian (SAS) AF: 0.837 AC: 4043 AN: 4832

European-Finnish (FIN) AF: 0.741 AC: 7861 AN: 10608

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.788 AC: 53632 AN: 68022

Other (OTH) AF: 0.853 AC: 1804 AN: 2114

Alfa AF: 0.801 Hom.: 6123

Bravo AF: 0.860

Asia WGS AF: 0.868 AC: 3016 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.41
DANN	Benign	0.65
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs2153101; hg19: chr1-203168474;