1-113994158-C-T

Position:

• chr1-113994158-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 0.0976 in 152,266 control chromosomes in the GnomAD database, including 1,165 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 0.098 (1165 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.113994158C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OLFML3	ENST00000633022.1	n.118+13541C>T		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.0977 AC: 14864 AN: 152148 Hom.: 1164 Cov.: 32

Gnomad AFR AF: 0.0227

Gnomad AMI AF: 0.0945

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.0923

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0989

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.0976 AC: 14866 AN: 152266 Hom.: 1165 Cov.: 32 AF XY: 0.103 AC XY: 7639 AN XY: 74444

Gnomad4 AFR AF: 0.0227

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.442

Gnomad4 SAS AF: 0.0930

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.0990

Gnomad4 OTH AF: 0.108

Alfa AF: 0.0945 Hom.: 356

Bravo AF: 0.0992

Asia WGS AF: 0.239 AC: 830 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.9
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12029644; hg19: chr1-114536780;