rs9971686

Positions:

• chr12-8600743-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 0.174 in 152,124 control chromosomes in the GnomAD database, including 3,020 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 0.17 (3020 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.803

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.317 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: 0.174 AC: 26453 AN: 152006 Hom.: 3006 Cov.: 31

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.0550

Gnomad SAS AF: 0.0288

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.174 AC: 26501 AN: 152124 Hom.: 3020 Cov.: 31 AF XY: 0.171 AC XY: 12741 AN XY: 74368

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.0553

Gnomad4 SAS AF: 0.0290

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.162

Alfa AF: 0.171 Hom.: 482

Bravo AF: 0.182

Asia WGS AF: 0.0660 AC: 229 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9971686; hg19: chr12-8753339;