rs17259942

chr12-76678297-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 0.0996 in 152,232 control chromosomes in the GnomAD database, including 890 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 (890 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.604

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.12 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: 0.0996 AC: 15151 AN: 152114 Hom.: 887 Cov.: 32

Gnomad AFR AF: 0.0589

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0793

Gnomad EAS AF: 0.0121

Gnomad SAS AF: 0.0590

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.0573

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.0995

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

GnomAD4 genome AF: 0.0996 AC: 15159 AN: 152232 Hom.: 890 Cov.: 32 AF XY: 0.101 AC XY: 7526 AN XY: 74434

Gnomad4 AFR AF: 0.0588

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.0793

Gnomad4 EAS AF: 0.0122

Gnomad4 SAS AF: 0.0584

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.0980

Alfa AF: 0.111 Hom.: 195

Bravo AF: 0.0939

Asia WGS AF: 0.0590 AC: 205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	7.2
Dann	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17259942; hg19: chr12-77072077;