1-109278685-G-T

Variant names:

• chr1-109278685-G-T
• rs583104

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 0.638 in 152,220 control chromosomes in the GnomAD database, including 34,988 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 0.64 (34988 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.901 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: 0.638 AC: 97022 AN: 152102 Hom.: 34988 Cov.: 34

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.660

Gnomad AMR AF: 0.735

Gnomad ASJ AF: 0.827

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.684

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

GnomAD4 genome AF: 0.638 AC: 97042 AN: 152220 Hom.: 34988 Cov.: 34 AF XY: 0.641 AC XY: 47737 AN XY: 74434

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.735

Gnomad4 ASJ AF: 0.827

Gnomad4 EAS AF: 0.923

Gnomad4 SAS AF: 0.746

Gnomad4 FIN AF: 0.775

Gnomad4 NFE AF: 0.773

Gnomad4 OTH AF: 0.687

Alfa AF: 0.638 Hom.: 5664

Bravo AF: 0.618

Asia WGS AF: 0.789 AC: 2745 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.5
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs583104; hg19: chr1-109821307;