rs2165207

Positions:

• chr12-73738488-A-C
• chr12-73738488-A-G

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 0.41 in 151,434 control chromosomes in the GnomAD database, including 13,819 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 0.41 (13819 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.73738488A>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62054 AN: 151316 Hom.: 13803 Cov.: 30

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.410 AC: 62109 AN: 151434 Hom.: 13819 Cov.: 30 AF XY: 0.404 AC XY: 29867 AN XY: 73924

Gnomad4 AFR AF: 0.581

Gnomad4 AMR AF: 0.329

Gnomad4 ASJ AF: 0.347

Gnomad4 EAS AF: 0.155

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.370

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.372

Alfa AF: 0.220 Hom.: 450

Bravo AF: 0.419

Asia WGS AF: 0.235 AC: 819 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.57
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2165207; hg19: chr12-74132268;