rs1154865

Variant names:

• chr12-73596057-C-G
• rs1154865

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 0.223 in 151,974 control chromosomes in the GnomAD database, including 3,913 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 0.22 (3913 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.156

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.276 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: 0.223 AC: 33841 AN: 151856 Hom.: 3908 Cov.: 33

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.223 AC: 33855 AN: 151974 Hom.: 3913 Cov.: 33 AF XY: 0.224 AC XY: 16631 AN XY: 74300

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.225

Gnomad4 EAS AF: 0.131

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.217

Gnomad4 OTH AF: 0.213

Alfa AF: 0.214 Hom.: 460

Bravo AF: 0.230

Asia WGS AF: 0.141 AC: 495 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1154865; hg19: chr12-73989837; COSMIC: COSV52393682;