chr1-113916573-C-T

Position:

• chr1-113916573-C-T

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 0.195 in 152,128 control chromosomes in the GnomAD database, including 3,677 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 0.19 (3677 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.615

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.254 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: 0.195 AC: 29588 AN: 152010 Hom.: 3676 Cov.: 31

Gnomad AFR AF: 0.0450

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.195 AC: 29589 AN: 152128 Hom.: 3677 Cov.: 31 AF XY: 0.199 AC XY: 14774 AN XY: 74358

Gnomad4 AFR AF: 0.0448

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.251

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.358

Gnomad4 NFE AF: 0.257

Gnomad4 OTH AF: 0.186

Alfa AF: 0.230 Hom.: 2309

Bravo AF: 0.178

Asia WGS AF: 0.205 AC: 714 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.6
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs878129; hg19: chr1-114459195;