rs1145212

Variant names:

• chr11-116686149-G-A
• rs1145212

Your query was ambiguous. Multiple possible variants found:

• chr11-116686149-G-A
• chr11-116686149-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;