1-115038110-T-C

Position:

• chr1-115038110-T-C

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 0.414 in 151,986 control chromosomes in the GnomAD database, including 13,264 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 0.41 (13264 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.306

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.509 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: 0.414 AC: 62845 AN: 151868 Hom.: 13249 Cov.: 31

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.414 AC: 62907 AN: 151986 Hom.: 13264 Cov.: 31 AF XY: 0.420 AC XY: 31218 AN XY: 74270

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.320

Gnomad4 EAS AF: 0.485

Gnomad4 SAS AF: 0.526

Gnomad4 FIN AF: 0.504

Gnomad4 NFE AF: 0.397

Gnomad4 OTH AF: 0.380

Alfa AF: 0.360 Hom.: 2779

Bravo AF: 0.409

Asia WGS AF: 0.536 AC: 1861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.1
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12046203; hg19: chr1-115580731;