rs17043088

chr12-77185807-T-C

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 0.0847 in 152,218 control chromosomes in the GnomAD database, including 1,236 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 0.085 (1236 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.233 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: 0.0846 AC: 12868 AN: 152100 Hom.: 1233 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0443

Gnomad ASJ AF: 0.0444

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0130

Gnomad FIN AF: 0.0185

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0263

Gnomad OTH AF: 0.0751

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

GnomAD4 genome AF: 0.0847 AC: 12896 AN: 152218 Hom.: 1236 Cov.: 32 AF XY: 0.0814 AC XY: 6062 AN XY: 74444

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.0442

Gnomad4 ASJ AF: 0.0444

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0130

Gnomad4 FIN AF: 0.0185

Gnomad4 NFE AF: 0.0263

Gnomad4 OTH AF: 0.0734

Alfa AF: 0.0354 Hom.: 428

Bravo AF: 0.0951

Asia WGS AF: 0.0240 AC: 83 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.9
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: rs17043088; hg19: chr12-77579587;