chr1-109276674-C-A

Position:

• chr1-109276674-C-A

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 151,856 control chromosomes in the GnomAD database, including 26,718 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 (26718 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.763

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	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.550 AC: 83446 AN: 151738 Hom.: 26710 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.932

Gnomad SAS AF: 0.731

Gnomad FIN AF: 0.650

Gnomad MID AF: 0.774

Gnomad NFE AF: 0.669

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.550 AC: 83468 AN: 151856 Hom.: 26718 Cov.: 32 AF XY: 0.554 AC XY: 41121 AN XY: 74230

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.660

Gnomad4 ASJ AF: 0.668

Gnomad4 EAS AF: 0.932

Gnomad4 SAS AF: 0.732

Gnomad4 FIN AF: 0.650

Gnomad4 NFE AF: 0.669

Gnomad4 OTH AF: 0.594

Alfa AF: 0.465 Hom.: 1512

Bravo AF: 0.534

Asia WGS AF: 0.788 AC: 2741 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	0.54
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3902354; hg19: chr1-109819296;