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. The variant received -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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.573 AC: 23691 AN: 41378

American (AMR) AF: 0.494 AC: 7531 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1278 AN: 3468

East Asian (EAS) AF: 0.479 AC: 2462 AN: 5136

South Asian (SAS) AF: 0.375 AC: 1804 AN: 4814

European-Finnish (FIN) AF: 0.394 AC: 4142 AN: 10526

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.366 AC: 24855 AN: 67926

Other (OTH) AF: 0.463 AC: 977 AN: 2108

Alfa AF: 0.393 Hom.: 20810

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
PhyloP100		1.9

Splicing

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

Other links and lift over

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