rs17714469

chr12-91101386-G-A

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 0.0785 in 152,102 control chromosomes in the GnomAD database, including 585 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 0.078 (585 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.11 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: 0.0785 AC: 11925 AN: 151984 Hom.: 583 Cov.: 32

Gnomad AFR AF: 0.0321

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.0899

Gnomad ASJ AF: 0.0989

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0404

Gnomad FIN AF: 0.0726

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.0906

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

GnomAD4 genome AF: 0.0785 AC: 11933 AN: 152102 Hom.: 585 Cov.: 32 AF XY: 0.0773 AC XY: 5743 AN XY: 74342

Gnomad4 AFR AF: 0.0321

Gnomad4 AMR AF: 0.0902

Gnomad4 ASJ AF: 0.0989

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0408

Gnomad4 FIN AF: 0.0726

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.0901

Alfa AF: 0.0946 Hom.: 94

Bravo AF: 0.0775

Asia WGS AF: 0.0240 AC: 84 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.49
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17714469; hg19: chr12-91495163; COSMIC: COSV57128351;