1-109908341-G-C

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 0.358 in 151,904 control chromosomes in the GnomAD database, including 10,662 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 0.36 (10662 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.28

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 = 0.674 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: 0.358 AC: 54371 AN: 151786 Hom.: 10646 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.693

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.358 AC: 54422 AN: 151904 Hom.: 10662 Cov.: 32 AF XY: 0.366 AC XY: 27162 AN XY: 74222

Gnomad4 AFR AF: 0.253

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.693

Gnomad4 SAS AF: 0.543

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.353

Gnomad4 OTH AF: 0.407

Alfa AF: 0.148 Hom.: 208

Bravo AF: 0.366

Asia WGS AF: 0.575 AC: 1995 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.016
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3093054; hg19: chr1-110450963;