chr1-109908341-G-C

Variant names:

• chr1-109908341-G-C
• rs3093054

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;