rs9971637

Positions:

• chr12-17220805-G-A
• chr12-17220805-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.139 in 151,412 control chromosomes in the GnomAD database, including 2,659 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 0.14 (2659 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.787

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20929 AN: 151292 Hom.: 2634 Cov.: 32

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.0374

Gnomad AMR AF: 0.0726

Gnomad ASJ AF: 0.0381

Gnomad EAS AF: 0.0865

Gnomad SAS AF: 0.0577

Gnomad FIN AF: 0.0867

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.0534

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.139 AC: 20989 AN: 151412 Hom.: 2659 Cov.: 32 AF XY: 0.138 AC XY: 10195 AN XY: 73970

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.0724

Gnomad4 ASJ AF: 0.0381

Gnomad4 EAS AF: 0.0863

Gnomad4 SAS AF: 0.0573

Gnomad4 FIN AF: 0.0867

Gnomad4 NFE AF: 0.0534

Gnomad4 OTH AF: 0.111

Alfa AF: 0.0611 Hom.: 563

Bravo AF: 0.145

Asia WGS AF: 0.100 AC: 349 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	14
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9971637; hg19: chr12-17373739;