1-115586350-C-T

Position:

• chr1-115586350-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 0.228 in 152,136 control chromosomes in the GnomAD database, including 4,320 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 0.23 (4320 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.478

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34702 AN: 152018 Hom.: 4318 Cov.: 33

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.228 AC: 34727 AN: 152136 Hom.: 4320 Cov.: 33 AF XY: 0.239 AC XY: 17743 AN XY: 74354

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.330

Gnomad4 SAS AF: 0.401

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.217

Alfa AF: 0.183 Hom.: 1499

Bravo AF: 0.222

Asia WGS AF: 0.359 AC: 1244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4564142; hg19: chr1-116128971;