chr1-20588679-C-T

Variant names:

• chr1-20588679-C-T
• rs532545

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 0.246 in 152,214 control chromosomes in the GnomAD database, including 5,647 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 0.25 (5647 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295
• Publications: 52 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37376 AN: 152096 Hom.: 5646 Cov.: 32

Gnomad AFR AF: 0.0854

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.246 AC: 37379 AN: 152214 Hom.: 5647 Cov.: 32 AF XY: 0.242 AC XY: 17976 AN XY: 74410

African (AFR) AF: 0.0852 AC: 3540 AN: 41556

American (AMR) AF: 0.325 AC: 4967 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1422 AN: 3466

East Asian (EAS) AF: 0.133 AC: 689 AN: 5176

South Asian (SAS) AF: 0.216 AC: 1045 AN: 4830

European-Finnish (FIN) AF: 0.212 AC: 2244 AN: 10592

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.330 AC: 22429 AN: 67978

Other (OTH) AF: 0.282 AC: 595 AN: 2112

Alfa AF: 0.305 Hom.: 23540

Bravo AF: 0.247

Asia WGS AF: 0.187 AC: 649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	9.9
DANN	Benign	0.67
PhyloP100		-0.29
PromoterAI		-0.018	Neutral

Splicing

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

Other links and lift over

dbSNP: rs532545; hg19: chr1-20915172;