rs1145212

chr11-116686149-G-Achr11-116686149-G-T

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 0.443 in 151,814 control chromosomes in the GnomAD database, including 15,516 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 0.44 (15516 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.93

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.566 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: 0.443 AC: 67136 AN: 151696 Hom.: 15470 Cov.: 31

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.443 AC: 67250 AN: 151814 Hom.: 15516 Cov.: 31 AF XY: 0.442 AC XY: 32778 AN XY: 74156

Gnomad4 AFR AF: 0.573

Gnomad4 AMR AF: 0.494

Gnomad4 ASJ AF: 0.369

Gnomad4 EAS AF: 0.479

Gnomad4 SAS AF: 0.375

Gnomad4 FIN AF: 0.394

Gnomad4 NFE AF: 0.366

Gnomad4 OTH AF: 0.463

Alfa AF: 0.384 Hom.: 15633

Bravo AF: 0.460

Asia WGS AF: 0.458 AC: 1594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	7.5
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1145212; hg19: chr11-116556865; COSMIC: COSV55552155;