chr1-111114487-C-T

Variant names:

• chr1-111114487-C-T
• rs325910

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 0.249 in 152,100 control chromosomes in the GnomAD database, including 5,826 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 0.25 (5826 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.412 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: 0.248 AC: 37767 AN: 151982 Hom.: 5794 Cov.: 32

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.249 AC: 37854 AN: 152100 Hom.: 5826 Cov.: 32 AF XY: 0.253 AC XY: 18847 AN XY: 74374

Gnomad4 AFR AF: 0.418

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.251

Alfa AF: 0.0978 Hom.: 146

Bravo AF: 0.261

Asia WGS AF: 0.384 AC: 1340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.54
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs325910; hg19: chr1-111657109;