chr1-115038110-T-C

Variant names:

• chr1-115038110-T-C
• rs12046203

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.382 AC: 15851 AN: 41472

American (AMR) AF: 0.472 AC: 7209 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 1110 AN: 3464

East Asian (EAS) AF: 0.485 AC: 2501 AN: 5152

South Asian (SAS) AF: 0.526 AC: 2539 AN: 4824

European-Finnish (FIN) AF: 0.504 AC: 5313 AN: 10546

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.397 AC: 27008 AN: 67950

Other (OTH) AF: 0.380 AC: 802 AN: 2108

Alfa AF: 0.380 Hom.: 5329

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
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs12046203; hg19: chr1-115580731;