rs12118636

Variant names:

• chr1-52610487-G-A
• rs12118636

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 0.0711 in 152,074 control chromosomes in the GnomAD database, including 397 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 0.071 (397 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0939 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: 0.0711 AC: 10804 AN: 151956 Hom.: 398 Cov.: 31

Gnomad AFR AF: 0.0964

Gnomad AMI AF: 0.0198

Gnomad AMR AF: 0.0601

Gnomad ASJ AF: 0.0311

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0344

Gnomad FIN AF: 0.0931

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0656

Gnomad OTH AF: 0.0681

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

GnomAD4 genome AF: 0.0711 AC: 10811 AN: 152074 Hom.: 397 Cov.: 31 AF XY: 0.0709 AC XY: 5271 AN XY: 74322

Gnomad4 AFR AF: 0.0964

Gnomad4 AMR AF: 0.0600

Gnomad4 ASJ AF: 0.0311

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0341

Gnomad4 FIN AF: 0.0931

Gnomad4 NFE AF: 0.0656

Gnomad4 OTH AF: 0.0674

Alfa AF: 0.0686 Hom.: 106

Bravo AF: 0.0671

Asia WGS AF: 0.0170 AC: 60 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.1
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12118636; hg19: chr1-53076159;