rs11172290

chr12-57661710-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 0.172 in 152,188 control chromosomes in the GnomAD database, including 2,540 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 (2540 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.241 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: 0.172 AC: 26205 AN: 152070 Hom.: 2534 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.0976

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.172 AC: 26223 AN: 152188 Hom.: 2540 Cov.: 32 AF XY: 0.170 AC XY: 12643 AN XY: 74414

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.0976

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.159

Alfa AF: 0.185 Hom.: 550

Bravo AF: 0.176

Asia WGS AF: 0.126 AC: 438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	3.1
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11172290; hg19: chr12-58055493;