1-109279175-G-A

Position:

• chr1-109279175-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.74 (30653 hom., cov: 15)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.447

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.911 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.737 AC: 84268 AN: 114284 Hom.: 30656 Cov.: 15

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.786

Gnomad ASJ AF: 0.850

Gnomad EAS AF: 0.935

Gnomad SAS AF: 0.796

Gnomad FIN AF: 0.808

Gnomad MID AF: 0.876

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.751

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

GnomAD4 genome AF: 0.737 AC: 84266 AN: 114310 Hom.: 30653 Cov.: 15 AF XY: 0.736 AC XY: 39610 AN XY: 53796

Gnomad4 AFR AF: 0.431

Gnomad4 AMR AF: 0.786

Gnomad4 ASJ AF: 0.850

Gnomad4 EAS AF: 0.935

Gnomad4 SAS AF: 0.795

Gnomad4 FIN AF: 0.808

Gnomad4 NFE AF: 0.803

Gnomad4 OTH AF: 0.753

Alfa AF: 0.650 Hom.: 3975

Bravo AF: 0.620

Asia WGS AF: 0.808 AC: 2797 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.93
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4970836; hg19: chr1-109821797;