rs12118297

chr1-87313534-G-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 0.194 in 152,184 control chromosomes in the GnomAD database, including 3,031 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 (3031 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.385

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.314 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: 0.194 AC: 29544 AN: 152066 Hom.: 3025 Cov.: 33

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.194 AC: 29561 AN: 152184 Hom.: 3031 Cov.: 33 AF XY: 0.200 AC XY: 14886 AN XY: 74380

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.327

Gnomad4 SAS AF: 0.271

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.179

Gnomad4 OTH AF: 0.185

Alfa AF: 0.179 Hom.: 481

Bravo AF: 0.186

Asia WGS AF: 0.292 AC: 1016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.46
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12118297; hg19: chr1-87779217;