chr1-104231287-G-T

Variant names:

• chr1-104231287-G-T
• rs1928324

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 0.534 in 151,956 control chromosomes in the GnomAD database, including 22,876 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 (22876 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.604 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: 0.534 AC: 81082 AN: 151838 Hom.: 22866 Cov.: 33

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.534 AC: 81123 AN: 151956 Hom.: 22876 Cov.: 33 AF XY: 0.538 AC XY: 39998 AN XY: 74292

African (AFR) AF: 0.349 AC: 14466 AN: 41408

American (AMR) AF: 0.572 AC: 8730 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.661 AC: 2296 AN: 3472

East Asian (EAS) AF: 0.534 AC: 2759 AN: 5170

South Asian (SAS) AF: 0.613 AC: 2958 AN: 4826

European-Finnish (FIN) AF: 0.637 AC: 6722 AN: 10548

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.609 AC: 41356 AN: 67952

Other (OTH) AF: 0.536 AC: 1131 AN: 2112

Alfa AF: 0.453 Hom.: 1524

Bravo AF: 0.517

Asia WGS AF: 0.527 AC: 1838 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.30
DANN	Benign	0.19
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1928324; hg19: chr1-104773909;