rs12118390

Positions:

• chr1-80445429-G-A

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 0.0497 in 152,114 control chromosomes in the GnomAD database, including 419 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 0.050 (419 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.967

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.139 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: 0.0496 AC: 7543 AN: 151996 Hom.: 419 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.0226

Gnomad ASJ AF: 0.0112

Gnomad EAS AF: 0.0219

Gnomad SAS AF: 0.0131

Gnomad FIN AF: 0.0157

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0111

Gnomad OTH AF: 0.0378

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

GnomAD4 genome AF: 0.0497 AC: 7559 AN: 152114 Hom.: 419 Cov.: 32 AF XY: 0.0489 AC XY: 3639 AN XY: 74368

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.0225

Gnomad4 ASJ AF: 0.0112

Gnomad4 EAS AF: 0.0219

Gnomad4 SAS AF: 0.0131

Gnomad4 FIN AF: 0.0157

Gnomad4 NFE AF: 0.0111

Gnomad4 OTH AF: 0.0374

Alfa AF: 0.0187 Hom.: 121

Bravo AF: 0.0549

Asia WGS AF: 0.0200 AC: 68 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.3
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12118390; hg19: chr1-80911114;