rs2102755

Variant names:

• chr12-73235876-C-T
• rs2102755

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 0.101 in 152,196 control chromosomes in the GnomAD database, including 1,028 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 0.10 (1028 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

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 = 0.17 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: 0.101 AC: 15299 AN: 152078 Hom.: 1022 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.0945

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.0441

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.0480

Gnomad FIN AF: 0.0794

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0537

Gnomad OTH AF: 0.0798

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

GnomAD4 genome AF: 0.101 AC: 15325 AN: 152196 Hom.: 1028 Cov.: 32 AF XY: 0.102 AC XY: 7596 AN XY: 74410

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.0441

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.0479

Gnomad4 FIN AF: 0.0794

Gnomad4 NFE AF: 0.0537

Gnomad4 OTH AF: 0.0781

Alfa AF: 0.0708 Hom.: 535

Bravo AF: 0.114

Asia WGS AF: 0.0990 AC: 346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.9
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2102755; hg19: chr12-73629656;