1-109279386-G-T

Position:

• chr1-109279386-G-T

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 0.55 in 150,850 control chromosomes in the GnomAD database, including 26,513 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 0.55 (26513 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.91 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.550 AC: 82880 AN: 150732 Hom.: 26504 Cov.: 27

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.931

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.784

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.550 AC: 82903 AN: 150850 Hom.: 26513 Cov.: 27 AF XY: 0.554 AC XY: 40770 AN XY: 73616

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.660

Gnomad4 ASJ AF: 0.665

Gnomad4 EAS AF: 0.932

Gnomad4 SAS AF: 0.731

Gnomad4 FIN AF: 0.653

Gnomad4 NFE AF: 0.668

Gnomad4 OTH AF: 0.596

Alfa AF: 0.464 Hom.: 1505

Bravo AF: 0.533

Asia WGS AF: 0.791 AC: 2750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.8
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4970837; hg19: chr1-109822008;