rs2165207

Variant names:

• chr12-73738488-A-C
• rs2165207

Your query was ambiguous. Multiple possible variants found:

• 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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;