rs12118636

chr1-52610487-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 0.0711 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;