1-39598989-G-T

Variant names:

• chr1-39598989-G-T
• rs2746050

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 0.529 in 151,952 control chromosomes in the GnomAD database, including 23,154 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 0.53 (23154 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.669
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80218 AN: 151834 Hom.: 23102 Cov.: 32

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.529 AC: 80332 AN: 151952 Hom.: 23154 Cov.: 32 AF XY: 0.521 AC XY: 38683 AN XY: 74272

African (AFR) AF: 0.772 AC: 32019 AN: 41476

American (AMR) AF: 0.470 AC: 7181 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1419 AN: 3462

East Asian (EAS) AF: 0.493 AC: 2544 AN: 5164

South Asian (SAS) AF: 0.226 AC: 1085 AN: 4810

European-Finnish (FIN) AF: 0.454 AC: 4777 AN: 10532

Middle Eastern (MID) AF: 0.469 AC: 137 AN: 292

European-Non Finnish (NFE) AF: 0.438 AC: 29742 AN: 67934

Other (OTH) AF: 0.520 AC: 1097 AN: 2108

Alfa AF: 0.488 Hom.: 2664

Bravo AF: 0.550

Asia WGS AF: 0.421 AC: 1466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.64
DANN	Benign	0.48
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs2746050; hg19: chr1-40064661;