1-104231287-G-T

Variant names:

• chr1-104231287-G-T
• rs1928324

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.534 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

Gnomad4 AFR AF: 0.349

Gnomad4 AMR AF: 0.572

Gnomad4 ASJ AF: 0.661

Gnomad4 EAS AF: 0.534

Gnomad4 SAS AF: 0.613

Gnomad4 FIN AF: 0.637

Gnomad4 NFE AF: 0.609

Gnomad4 OTH AF: 0.536

Alfa AF: 0.463 Hom.: 1476

Bravo AF: 0.517

Asia WGS AF: 0.527 AC: 1838 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1928324; hg19: chr1-104773909;